Methods and compositions for treating ulcerative colitis

ABSTRACT

The present disclosure provides methods and pharmaceutical compositions for treating ulcerative colitis (UC) in a subject in need thereof In particular, the compositions described here comprise or are designed based on fecal bacteria associated with FMT-based UC treatment success or failure. Also provided are methods for screening patients for their suitability for a fecal bacteria-based UC treatment. Further provided are methods for screening fecal donors for optimized source materials for producing a fecal bacteria-based pharmaceutical composition.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Ser.Nos. 62/697,796 and 62/697,810, both filed Jul. 13, 2018, both of whichare incorporated herein by reference in their entirety.

FIELD

The present disclosure includes and relates to methods andpharmaceutical compositions suitable for treating ulcerative colitis ina subject in need thereof.

BACKGROUND

Mammals harbor diverse microbial species in their gastrointestinal (GI)tracts. Interactions between these microbes and between microbes and thehost, e.g. the host immune system, shape a microbiota. A healthymicrobiota provides the host with multiple benefits, includingcolonization resistance to a broad spectrum of pathogens, essentialnutrient biosynthesis and absorption, and immune stimulation thatmaintains a healthy gut epithelium and an appropriately controlledsystemic immunity. An unbalanced microbiota (also called ‘dysbiosis’ ordisrupted symbiosis) may lose its function and results in increasedsusceptibility to pathogens, altered metabolic profiles, or induction ofproinflammatory signals that can lead to local or systemic inflammationor autoimmunity. The intestinal microbiota play a role in thepathogenesis of many disorders such as pathogenic infections of the gut.

Ulcerative colitis (UC) is a chronic disease of the large intestine,also known as the colon, in which the lining of the colon becomesinflamed and develops tiny open sores, or ulcers, that produce pus andmucous. Ulcerative colitis occurs most often in people ages 15 to 30,although the disease may afflict people of any age. It affects men andwomen equally and appears to run in some families.

Ulcerative colitis is a disease that is characterized by inflammationand micro-ulcers in the superficial layers of the large intestine. Theinflammation usually occurs in the rectum and lower part of the colon,but it may affect the entire large intestine (pancolitis). Ulcerativecolitis can very rarely affect the small intestine in its distal portion(Backwash Ileitis).

The inflammation is accompanied usually with diarrhea, which may beprofuse and bloody. Micro-ulcers form in places where inflammation hasdestroyed the cells lining the bowel and these areas bleed and producepus and mucus. Ulcerative colitis, especially when mild, can bedifficult to diagnose because symptoms are similar to other intestinaldisorders, most notably the other type of Irritable Bowel Diseases (IBD)called Crohn's disease and also irritable bowel syndrome. Crohn'sdisease differs from ulcerative colitis because it causes inflammationthroughout the whole thickness of the intestinal wall and produces deepulcers. Crohn's disease usually occurs in the small intestine, but itcan also occur in the large intestine, anus, esophagus, stomach,appendix and mouth. Crohn's disease causes fistulae whereas ulcerativecolitis does not. Both Crohn's and ulcerative colitis may co-exist inthe same patient. The combination of inflammation and ulceration cancause abdominal discomfort and frequent emptying of the colon. Existingtreatments for ulcerative colitis involve intense and lengthycombinational drug therapy with side effects or even require surgery toremove part of the colon. Moreover, a substantial proportion ofulcerative colitis patients are resistant to standard drug therapy.Thus, there is a need for more effective treatments for ulcerativecolitis that are easier to administer.

SUMMARY

The present disclosure provides methods and compositions for treating orpreventing ulcerative colitis.

In an aspect, this application provides a pharmaceutical compositioncomprising viable non-pathogenic bacteria from one or more firstmicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia, Eubacterium hallii, andany combination thereof, wherein the pharmaceutical composition containsno bacteria from one or more second microbial taxa selected from thegroup consisting of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila.

In an aspect, this application provides a pharmaceutical compositioncomprising a substantially entire fecal microbiota supplemented,enhanced, or spiked with viable non-pathogenic bacteria from one or moremicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia, and Eubacterium hallii.

In an aspect, this application provides a pharmaceutical compositioncomprising a substantially entire fecal microbiota supplemented,enhanced, or spiked with viable non-pathogenic bacteria from a microbialtaxon selected from the group consisting of Bacteroides OTU187,Bacteroides fragilis, and Bacteroides finegoldii.

In an aspect, this application provides a pharmaceutical compositioncomprising a fecal microbiota preparation having a suppressed,decreased, reduced, minimized, or undetectable level of a microbialtaxon selected from the group consisting of Clostridium cluster XIVa(OTU173), Streptococcus (OTU56), Sutterella wadsworthensis, Bacteroidesuniformis, and Bacteroides coprocola.

In an aspect, this application provides a method for treating ulcerativecolitis (UC) in a patient in need thereof, the method comprisingadministering to the patient a pharmaceutical composition describedhere.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient ispretested for one or more markers from a metabolic pathway selected fromthe group consisting of benzoate degradation, glycerophospholipidmetabolism, secondary bile acid biosynthesis, ppGpp biosynthesis,pyruvate fermentation to acetate and lactate, short chain fatty acidbiosynthesis, biosynthesis of ansamycins, starch degradation, hemebiosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient ispretested for the relative abundance of Fusobacterium gonidiaformans,Prevotella copri, Sutterella wadsworthensis, or any combination thereof.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient comprisesa relative abundance of Fusobacterium gonidiaformans, Prevotella copri,or Sutterella wadsworthensis below a pre-determined highest limit.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient comprisesa relative abundance of one or more microbial taxa selected from thegroup consisting of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila, below a pre-determined highest limit.

DETAILED DESCRIPTION

A randomised controlled study (ClinicalTrials.gov: NCT01896635) showsthat multi-donor FMT therapy for active UC is significantly superior toplacebo with 27% of patients achieving the primary endpoint of clinicalremission with endoscopic remission or response compared to 7.5% withplacebo, and more than half of patients on active treatment gaining aclinical response. Here, Applicant provides bacterial taxonomic andfunctional changes associated with FMT in UC, particularly thosepredictive of therapeutic success or failure. Applicant furtherillustrates underlying microbial basis, predictors of therapeuticoutcome and the active constituent(s) of FMT mediating benefit.

Before the present compositions and methods are described, it is to beunderstood that the present disclosure is not limited to the particularprocesses, compositions, or methodologies described, as these may vary.It is also to be understood that the terminology used in the descriptionis for the purpose of describing the particular versions or embodimentsonly, and is not intended to limit the scope of the present inventionwhich will be limited only by the appended claims. For example, featuresillustrated with respect to one embodiment may be incorporated intoother embodiments, and features illustrated with respect to a particularembodiment may be deleted from that embodiment. Thus, the disclosurecontemplates that in some embodiments of the disclosure, any feature orcombination of features set forth herein can be excluded or omitted. Inaddition, numerous variations and additions to the various embodimentssuggested herein will be apparent to those skilled in the art in lightof the instant disclosure, which do not depart from the instantdisclosure. In other instances, well-known structures, interfaces, andprocesses have not been shown in detail in order not to unnecessarilyobscure the invention. It is intended that no part of this specificationbe construed to effect a disavowal of any part of the full scope of theinvention. Hence, the following descriptions are intended to illustratesome particular aspects of the disclosure, and not to exhaustivelyspecify all permutations, combinations and variations thereof.

Unless defined otherwise herein, terms are to be understood according toconventional usage by those of ordinary skill in the relevant art. Theterminology used in the description of the disclosure herein is for thepurpose of describing particular embodiments only and is not intended tobe limiting of the disclosure.

All publications, patent applications, patents and other referencescited herein are incorporated by reference in their entireties.

Unless the context indicates otherwise, it is specifically intended thatthe various features of the disclosure described herein can be used inany combination. Moreover, the present disclosure also contemplates thatin some embodiments of the disclosure, any feature or combination offeatures set forth herein can be excluded or omitted.

Methods disclosed herein can comprise one or more steps or actions forachieving the described method. The method steps and/or actions may beinterchanged with one another without departing from the scope of thepresent invention. In other words, unless a specific order of steps oractions is required for proper operation of the embodiment, the orderand/or use of specific steps and/or actions may be modified withoutdeparting from the scope of the present invention.

As used in the description of the disclosure and the appended claims,the singular forms “a,” “an” and “the” are intended to include theplural forms as well, unless the context clearly indicates otherwise.

As used herein, “and/or” refers to and encompasses any and all possiblecombinations of one or more of the associated listed items, as well asthe lack of combinations when interpreted in the alternative (“or”).

The terms “about” and “approximately” as used herein when referring to ameasurable value such as a percentages, density, volume and the like, ismeant to encompass variations of 20%, 10%, 5%, 1%, 0.5%, or even 0.1% ofthe specified amount.

As used herein, the term “substantially”, when used to modify a quality,generally allows certain degree of variation without that quality beinglost. For example, in certain aspects such degree of variation can beless than 0.1%, about 0.1%, about 0.2%, about 0.3%, about 0.4%, about0.5%, about 0.6%, about 0.7%, about 0.8%, about 0.9%, about 1%, between1-2%, between 2-3%, between 3-4%, between 4-5%, or greater than 5%.

As used herein, phrases such as “between X and Y” and “between about Xand Y” should be interpreted to include X and Y. As used herein, phrasessuch as “between about X and Y” mean “between about X and about Y” andphrases such as “from about X to Y” mean “from about X to about Y.”

As used herein, a “taxon” refers to a particular taxonomic grouping,e.g., a particular species, genus, family, order, class, or phylum. Theplural form of “taxon” is “taxa”.

As used herein, a “subtaxon” refers to a taxonomic grouping at a lowerlevel relative to and encompassed by a reference taxon. For example, allthe subspecies, species, and genera within a taxon of particular familywould be considered as a subtaxon of that family. The plural form of“subtaxon” is “subtaxa”.

In an aspect, a marker for a pathway or a taxon (e.g., a metabolicpathway biomarker or a microbial biomarker) comprises a nucleic acidmolecule, a peptide, a protein, a metabolite, a small molecule, amacromolecule, a secreted molecule, or a combination of any of theforegoing. In another aspect, a marker for a taxon comprises a 16S rDNAmolecule or a 16S rRNA molecule. A marker can be identified orcharacterized using many methods such as those for characterizingnucleic acid and/or proteins. Nucleic acid analysis includes analysisof, for example, DNA, RNA, mRNA, rRNA, and/or tRNA, and can beaccomplished using, for example, pyrosequencing, qPCR, RT-qPCR, clonelibraries, denaturing gradient gel electrophoresis (DGGE), Terminalrestriction fragment length polymorphism (T-RFLP), automated ribosomalintergenic spacer analysis (ARISA), microarrays, fluorescence in situhybridization (FISH), dot-blot hybridization, next generationsequencing, and any other DNA hybridization methods that will detect aspecific sequence. Protein analysis includes, for example, 2-DimensionalGel Electrophoresis, 2-Diminsional Difference Gel Electrophoresis(2D-DIGE), MALDI TOF- MS, (2D-) LC-ESI-MS/MS, absolute quantification(AQUA), and isobaric tags for relative and absolute quantitation(iTRAQ).

In an aspect, a marker for a metabolic pathway comprises a RNAtranscript molecule or a DNA molecule encoding an enzymatic polypeptide(or fragment thereof) from the metabolic pathway. In another aspect, amarker for a metabolic pathway comprises an enzymatic polypeptide (orfragment thereof) from the metabolic pathway. In an aspect, a marker fora metabolic pathway comprises an intermediary of the metabolic pathway.In an aspect, a marker for a metabolic pathway comprises the product ofthe metabolic pathway. For example, a marker for short chain fatty acidbiosynthesis can include one or more short chain fatty acids.

As used herein, a “short chain fatty acid” or “SCFA” refers to fattyacids with an aliphatic tail of one to six carbon atoms. SCFAs can beproduced by bacteria during bacterial metabolism, such as duringfermentation of, for example, carbohydrates, proteins, peptides andglycoprotein precursors. Illustrative SCFAs include, but are not limitedto, acetic acid (also known as acetate), butyric acid (also known asbutyrate), caproic acid (also known as hexanoic acid), formic acid (alsoknown as methanoic acid), heptanoic acid (also known as enanthic acid),isobutyric acid (also known as 2-methylpropanoic acid), isocaproic acid(also known as 4-methylpentanoic acid or 4-methylvaleric acid),isovaleric acid (also known as 3-methylbutanoic acid or β-methylbutyricacid), propionic acid (also known as propanoic acid), and valeric acid(also known as pentanoic acid).

As used herein, a “bile acid” refers to hydroxylated steroidssynthesized from cholesterol in the liver, to break down fats. Examplesof bile acids are cholic acid and chenodeoxycholic acid. Bile acids areconjugated with glycine or taurine prior to secretion into the bile.There are at least five major bile acid forms. Bile acids can bemodified by intestinal bacteria. For example, primary bile acids areconverted to secondary bile acids by dehydroxylation. Examples ofsecondary bile acids include lithocholic acid, deoxycholic acid, andursodeoxycholic acid. Bile acids are reabsorbed by the entero-hepatictransport system and returned to the liver or excreted in feces.(Banerjee, A. Gastrointestinal toxicity biomarkers, Biomarkers inToxicology, (2014)). Additional examples of bile acids are glycocholicacid, glycohenodeoxycholic acid, taurocholic acid, andtaurochenodeoxycholic acid.

As used herein, “relative abundance” of a taxon within a communityrefers to the abundance of one taxon in comparison to other taxa presentin that community, and reflects the evenness of distribution ofindividuals among a community. Example 1 provides an exemplary way ofdetermining the relative abundance of a taxon of interest based on thenumber of 16S rDNA sequencing reads assigned to that taxon relative tothe overall number of 16S rDNA sequencing reads from all microbespresent in a community.

As used herein, “relative fecal abundance” refers to the relativeabundance of a molecule or entity in a feces.

As used herein, “relative abundance ratio” refers to the ratio betweenthe relative abundance of two or more taxa in comparison.

As used herein, the term “treating” refers to (i) completely orpartially inhibiting a disease, disorder or condition, for example,arresting its development; (ii) completely or partially relieving adisease, disorder or condition, for example, causing regression of thedisease, disorder and/or condition; or (iii) completely or partiallypreventing a disease, disorder or condition from occurring in a patientthat may be predisposed to the disease, disorder and/or condition, buthas not yet been diagnosed as having it. Similarly, “treatment” refersto both therapeutic treatment and prophylactic or preventative measures.

As used herein, a “therapeutically effective amount” or“pharmaceutically active dose” refers to an amount of a compositionwhich is effective in treating the named disease, disorder or condition.

As used herein, “microbiota” refers to a community of microbes thatviable in or on a patient's body, both sustainably and transiently,including eukaryotes, archaea, bacteria, and viruses (includingbacterial viruses (i.e., phage)). A non-selected fecal microbiota refersto a community or mixture of fecal microbes derived from a donor's fecalsample without selection and substantially resembling microbialconstituents and population structures found in such fecal sample.

As used herein, “remission rate,” “cure rate,” or “resolution rate”refers to the percentage of patients that are cured or obtain remissionor complete resolution of a condition in response to a given treatment.As used herein, “clinical remission sustaining rate” refers to thepercentage of patients remaining in clinical remission after a specifiedpost-treatment period among all patients who achieve remission at thecompletion of a treatment. Quantitatively, remission, cure, orresolution is achieved when a patient's UCDAI score is below or equal to2, assessed after 8 weeks of treatment. Remission, cure, or resolutioncan be further confirmed by endoscopic and mucosal healing.

As used herein, “primary outcome rate” refers to the percentage ofpatients achieving primary outcome after a specific treatment ortreatment regimen among all patients receiving that treatment ortreatment regimen.

As used herein, “response rate” refers to the percentage of patientsthat respond positively to a given treatment. Quantitatively, a patientresponds to a treatment positively when the patient's UCDAI scoredecreases by at least 2 from baseline to week 8.

As used herein, “Mayo Clinic score” or “Mayo score” refers to an indexsystem for assessing the severity of a ulcerative colitis diseasecondition. See Table 1 and Schoeder et al. N Engl J Med 1987;317:1625-9.The Mayo Clinic score ranges from 0-12, with sub-scores of 0-3, wherethe higher scores indicate more severe disease. In an aspect, sub-scoresmay be rated for stool frequency, rectal bleeding, mucosal appearance atendoscopy, and physician's global assessment (PGA).

TABLE 1 Mayo Clinic Scoring System for Assessment of Ulcerative ColitisActivity (Schoeder et al. N Engl J Med 1987; 317: 1625-9) scoreassignment 1. Stool frequency* Normal number of stools for this patient0 1-2 stools more than normal 1 3-4 stools more than normal 2 5 or morestools more than normal 3 2. Rectal Bleeding† No blood seen 0 Streaks ofblood with stool less half the time 1 Obvious blood with stool most ofthe time 2 Blood alone passed 3 3. Findings of flexibleproctosigmoidoscopy Normal or inactive disease 0 Mild disease (erythema,decreased vascular pattern, mild 1 friability) Moderate disease (markederythema, absent vascular 2 pattern, friability, erosions) Severedisease (spontaneous bleeding, ulceration) 3 4. Physician's globalassessment‡ Normal 0 Mild disease 1 Moderate disease 2 Severe disease 3*Each patient served as his or her own control to establish the degreeof abnormality of the stool frequency †The daily bleeding scorerepresented the most severe bleeding of the day ‡The physician's globalassessment acknowledged the three other criteria, the patient's dailyrecord of abdominal discomfort and general sense of well-being, andother observations, such as physical findings and the patient'sperformance status

As used herein, “ulcerative colitis endoscopic index of severity” or“UCEIS” refers to an index for assessing endoscopic disease activity.The index assesses three criteria, including vascular pattern, bleeding,and erosions and ulcers (Table 2). See Travis et al., Developing aninstrument to assess the endoscopic severity of ulcerative colitis: theUlcerative Colitis Endoscopic Index of Severity (UCEIS), Gut 2012,61(4): 535-42. A higher score reflects increased disease severity.

TABLE 2 Scoring System for Ulcerative Colitis Endoscopic Index ofSeverity (See Travis et al.) score assignment 1. Vascular patternNormal: Normal vascular pattern with arborization of 1 capillariesclearly defined, or with blurring or patchy loss of capillary marginsPatchy obliteration: Patchy obliteration of vascular pattern 2Obliterated: Complete obliteration of vascular pattern 3 2. Rectalbleeding None: No visible blood 1 Mucosal: Some spots or streaks ofcoagulated blood on 2 the surface of the mucosa ahead of the scope,which can be washed away Luminal mild: Some free liquid blood in thelumen 3 Luminal moderate or severe: Frank blood in the lumen 4 ahead ofendoscope or visible oozing from mucosa after washing intra-luminalblood, or visible oozing from a hemorrhagic mucosa 3. Erosions andulcers None: Normal mucosa, nonvisible erosions or ulcers 1 Erosions:Tiny (≤5 mm) defects in the mucosa, of a 2 white or yellow color with aflat edge Superficial ulcer: Larger (>5 mm) defects in the mucosa, 3which are discrete fibrin-covered ulcers when compared to erosions, butremain superficial Deep ulcer: Deeper excavated defects in the mucosa,with a 4 slightly raised edge

As used herein, “ulcerative colitis disease activity index” or “UCDAI”refers to an index system for assessing the symptomatic severity orresponse of a ulcerative colitis patient. The index assesses fourvariables, which include stool frequency, severity of bleeding, colonicmucosal appearance, and the physician's overall assessment of diseaseactivity (Table 3). See Sutherland et al., 5-Aminosalicylic acid enemain the treatment of distal ulcerative colitis, proctosigmoiditis, andproctitis. Gastroenterology. 1987; 92:1 894-8. Each variable is scoredfrom 0-3 so that the total index score ranges from 0-12; 0-2: remission;3-6: mild; 7-10: moderate; >10: severe ulcerative colitis.

TABLE 3 Scoring System for Ulcerative Colitis Disease Activity Index.(See Tursi et al.) score assignment 1. Stool frequency Normal 0 1-2Stools/day>normal 1 3-4 Stools/day>normal 2 >4 Stools/day>normal 3 2.Rectal bleeding None 0 Streaks of blood 1 Obvious blood 2 Mostly blood 33. Mucosal appearance Normal 0 Mild friability 1 Moderate friability 2Exudation, spontaneous bleeding 3 4. Physician's rating of diseaseactivity Normal 0 Mild 1 Moderate 2 Severe 3

As used herein, “bacteria,” “bacterium,” and “archaea” refer tosingle-celled prokaryotes that lack membrane bound nuclei and lackorganelles.

As used herein, “fecal bacteria” refers to bacteria that can be found infecal matter.

As used herein, “viable” means possessing the ability to multiply.

As used herein, “isolated” or “purified” refers to a bacterium or otherentity or substance that has been (1) separated from at least some ofthe components with which it was associated when initially produced(whether in nature or in an experimental setting), and/or (2) produced,prepared, purified, and/or manufactured by the hand of man. Isolated orpurified bacteria can be separated from at least about 10%, about 20%,about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about90%, or more of the other components with which they were initiallyassociated.

As used herein, the terms “pathogen” and “pathogenic” in reference to abacterium or any other organism or entity includes any such organism orentity that is capable of causing or affecting a disease, disorder orcondition of a host organism containing the organism or entity.

As used herein, “spore” or a population of “spores” includes bacteria(or other single-celled organisms) that are generally viable, moreresistant to environmental influences such as heat and bacteriocidalagents than vegetative forms of the same bacteria, and typically capableof germination and out-growth. “Spore-formers” or bacteria “capable offorming spores” are those bacteria containing the genes and othernecessary abilities to produce spores under suitable environmentalconditions.

As used herein, a “combination” of two or more bacteria includes thephysical co-existence of the two bacteria, either in the same materialor product or in physically connected products, as well as the temporalco-administration or co-localization of the two bacteria.

As used herein, a “subject” refers to a human. A subject may be healthy,or may be suffering from an infection due to a gastrointestinal pathogenor may be at risk of developing or transmitting to others an infectiondue to a gastrointestinal pathogen.

As used herein, “operational taxonomic unit” or “OTU” refers to a groupof closely related microbial species determined based on 16S or 18S rRNAmarker genes. As illustrated in Example 1, in an aspect, an OTU canshare 97% similarity in 16S rRNA sequences based on a opti-clust averageneighbour algorithm.

As used herein, an “intermittent dosing schedule” means that apharmaceutical composition is administered for a period of time followedby a period of time (a treatment period) where treatment with suchpharmaceutical composition is withheld (a rest period). Intermittentdosing regimens can be expressed as treatment period in days orweeks/rest period in days or weeks. For example, a 4/1 intermittentdosing schedule refers to an intermittent dosing schedule where thetreatment period is four weeks/days and the rest period is one week/day.

As used herein, a “continuous dosing schedule” refers to a dosingschedule where a pharmaceutical composition is administered during atreatment period without a rest period. Throughout the treatment periodof a continuous dosing schedule, a pharmaceutical composition can beadministered, for example, daily, or every other day, or every thirdday. On a day when a pharmaceutical composition is administered, it canbe administered in a single dose, or in multiple doses throughout theday.

As used herein, “dosing frequency” refers to the frequency ofadministering doses of a pharmaceutical composition in a given time.Dosing frequency can be indicated as the number of doses per a giventime, for example, once per day, once a week, or once in two weeks.

As used herein, “dosing interval” refers to the amount of time thatelapses between multiple doses being administered to a patient.

Different types of ulcerative colitis exist. As used herein, “ulcerativeproctitis” refers to a disease form where bowel inflammation is limitedto the rectum. Because of its limited extent (usually less than the sixinches of the rectum), ulcerative proctitis tends to be a milder form ofulcerative colitis. It is associated with fewer complications and offersa better outlook than more widespread disease. For approximately 30% ofall patients with ulcerative colitis, the illness begins as ulcerativeproctitis.

As used herein, “proctosigmoiditis” refers to a form of colitisaffecting the rectum and the sigmoid colon, the lower segment of colonlocated right above the rectum. Symptoms include bloody diarrhea,cramps, and a constant feeling of the need to pass stool, known astenesmus. Moderate pain on the lower left side of the abdomen may occurin active disease.

As used herein, “left-sided colitis” refers to continuous inflammationthat begins at the rectum and extends as far as a bend in the colon nearthe spleen called the splenic flexure. Symptoms include loss ofappetite, weight loss, diarrhea, severe pain on the left side of theabdomen, and bleeding.

As used herein, “pan-ulcerative (total) colitis” affects the entirecolon.

Symptoms include diarrhea, severe abdominal pain, cramps, and extensiveweight loss. Potentially serious complications include massive bleedingand acute dilation of the colon (toxic megacolon), which may lead to anopening in the bowel wall. Serious complications may require surgery.

Several theories have been proposed for the cause of ulcerative colitis.There is some evidence to suggest that the body's immune system reactsto an environmental, dietary or infectious agent in geneticallysusceptible individuals causing inflammation in the intestinal wall. Thelatest postulated causal agent is the to be an infection of the liningwith a Fusobacterium varium identified by researchers from Japan.Ulcerative colitis is not caused by emotional distress or sensitivity tocertain foods or food products but these factors may trigger symptoms insome people. Ulcerative colitis is most likely not an aberrant reactionbut an infection.

The most common symptoms of ulcerative colitis are bloody diarrhea andabdominal pain. Patients also may experience fever, rectal bleeding,fatigue, anaemia, loss of appetite, weight loss and loss of body fluidsand nutrients resulting in nutritional deficiencies. These symptomsoccur as intermittent attacks in between periods when the symptoms goaway (remissions). These disease-free periods can last for months oreven years. Usually an attack begins with increased urgency to defecate,mild lower abdominal cramps, and blood and mucus in the stools.

Ulcerative colitis may cause long-term problems such as arthritis,inflammation of the eye, liver disease (fatty liver, hepatitis,cirrhosis, and primary sclerosing cholangitis), osteoporosis, skinrashes, anaemia and kidney stones. These complications may occur whenthe immune system triggers inflammation in other parts of the body.These problems can disappear when the colitis is treated effectively.

Treatment for ulcerative colitis depends on the seriousness of thedisease. Most people are treated with medication. Some people whosesymptoms are triggered by certain foods are able to control the symptomsby avoiding foods that upset their intestines, like highly seasonedfoods or dairy products. Each person may experience ulcerative colitisdifferently, so treatment is adjusted for each individual.

Many patients with mild or moderate disease are first treated with 5-ASAagents, including a combination of the drugs 5-aminosalicylic acids andsulfasalazine that helps control inflammation. Sulfasalazine is the mostcommonly used of these drugs. Sulfasalazine can be used for as long asneeded and can be given along with other drugs. Patients who do not dowell on sulfasalazine may respond to newer 5-ASA agents. Possible sideeffects of 5-ASA preparations include nausea, vomiting, heartburn,diarrhea and headache.

People with severe disease and those who do not respond to 5-ASApreparations may be treated with added corticosteroids. Prednisone andbudesonide and hydrocortisone are corticosteroids used to reduceinflammation. They can be given orally, intravenously, through an enema,or in a suppository, depending on the location of the inflammation.Corticosteroids can cause side effects such as weight gain, acne, facialhair, hypertension, diabetes, mood swings, and increased risk ofinfection, so doctors carefully monitor patients taking thesemedications.

Immunosuppressants such as azathioprine, 6-mercaptopurine (6-MP) andmethotrexate are often used and can make a marked improvement at a lowdose with few side effects. Other drugs may be given to relax thepatient or to relieve pain, diarrhea, or infection. Occasionally,symptoms are severe enough that the person must be hospitalized. Forexample, a person may have severe bleeding or severe diarrhea thatcauses dehydration. In such cases the doctor will try to stop diarrheaand loss of blood, fluids, and mineral salts. The patient may need aspecial diet, feeding through a vein, medications, or sometimes surgery.

In severe cases, a patient may need surgery to remove the diseasedcolon.

Sometimes the doctor will recommend removing the colon if medicaltreatment fails or if the side effects of corticosteroids or other drugsthreaten the patient's health.

In an aspect, this application provides a microbial biomarker and itsuse for predicting the likelihood of a UC patient achieving a primaryoutcome using a fecal bacteria-based therapy. In an aspect, thedisclosure provides a microbial taxon, or a subtaxon therein, in UCpatients associated with UC treatment success, where the microbial taxonis selected from the group consisting of Clostridium cluster XVIII,Ruminococcus, Lachnospiraceae, Roseburia inulinivorans, and Eubacteriumhallii.

In another aspect, this application provides a microbial biomarker andits use for screening a UC patient for the patient's suitability for afecal bacteria-based therapy. In an aspect, this application provide amicrobial taxon, or a subtaxon therein, in UC patients associated withlack of UC treatment success, where the microbial taxon is selected fromthe group consisting of Fusobacterium, Sutterella, Haemophilus,Escherichia, Megamonas, Clostridium cluster XIVa, Prevotella, Dialister,Veillonella, and Bilophila, or a subtaxon within the microbial taxon. Inanother aspect, this application provide a microbial taxon, or asubtaxon therein, in UC patients associated with lack of UC treatmentsuccess, where the microbial taxon is selected from the groupFusobacterium gonidiaformans, Prevotella copri, and Sutterellawadsworthensis.

In an aspect, this application provides a metabolic pathway biomarkerand its use for predicting the likelihood of a UC patient achieving aprimary outcome using a fecal bacteria-based therapy. In another aspect,a metabolic pathway biomarker associated with UC treatment success isselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, and starchdegradation.

In an aspect, this application provides a metabolic pathway biomarkerfor predicting the likelihood of a UC patient not achieving a primaryoutcome using a fecal bacteria-based therapy. In another aspect, ametabolic pathway biomarker associated with UC treatment failure isselected from the group consisting of heme biosynthesis,lipopolysaccharide biosynthesis, ubiquinone and other terpenoid quininebiosynthesis, lysine biosynthesis and oxidative phosphorylationpathways.

In another aspect, this application provides a biomarker and its use forpredicting the effectiveness of a donor fecal material for treating UC.In an aspect, a microbial taxon in donor fecal material associated witheffective UC treatment is selected from the group consisting ofBacteroides OTU187, Bacteroides fragilis, and Bacteroides finegoldii. Inanother aspect, a microbial taxon in donor fecal material associatedwith ineffective UC treatment is selected from the group consisting ofBacteroides uniformis, Bacteroides coprocola, Clostridium cluster XIVa(OTU173), Streptococcus (OTU56), and Sutterella wadsworthensis. In anaspect, a metabolic pathway in donor fecal material associated witheffective UC treatment is selected from the group consisting of fattyacid biosynthesis, propanoate metabolism, secondary bile acidbiosynthesis, glycerophospholipid metabolism, and biosynthesis ofansamycins. In an aspect, a metabolic pathway in donor fecal materialassociated with ineffective UC treatment is selected from the groupconsisting of terpenoid backbone biosynthesis, bacterial chemotaxis, andheme biosynthesis.

In an aspect, a marker in a patient indicating positive primary outcomecan also be a marker for selecting a successful source material from oneor more donors. In an aspect, a successful source material is derivedfrom one or more donors. In another aspect, a successful source materialis synthetic.

In an aspect, this application provides a method for selecting a sourcematerial from a donor based on a biomarker. In an aspect the sourcematerial is derived from fecal microbiota from a donor. In anotheraspect, the source material is derived from the fecal microbiota of oneor more donors. In yet another aspect, the source material is derivedfrom the fecal microbiota of two or more, three or more, four or more,or five or more donors. In a further aspect, the source material isderived from the fecal microbiota of a donor related to or unrelated tothe patient in need of the source material.

In an aspect a biomarker is one or more markers from a metabolic pathwayselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, starch degradation,heme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway. In another aspect, a biomarker is two or moremarkers from a metabolic pathway selected from the group consisting ofbenzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, starch degradation, heme biosynthesis, lipopolysaccharidebiosynthesis, ubiquinone and other terpenoid quinine biosynthesis,lysine biosynthesis, and oxidative phosphorylation pathway. In anotheraspect, a biomarker is three or more markers from a metabolic pathwayselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, starch degradation,heme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway. In a further aspect, a biomarker is four ormore markers from a metabolic pathway selected from the group consistingof benzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, starch degradation, heme biosynthesis, lipopolysaccharidebiosynthesis, ubiquinone and other terpenoid quinine biosynthesis,lysine biosynthesis, and oxidative phosphorylation pathway. In anotheraspect, a biomarker is five or more markers from a metabolic pathwayselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, starch degradation,heme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway. In another aspect, a biomarker is six or moremarkers from a metabolic pathway selected from the group consisting ofbenzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, starch degradation, heme biosynthesis, lipopolysaccharidebiosynthesis, ubiquinone and other terpenoid quinine biosynthesis,lysine biosynthesis, and oxidative phosphorylation pathway. In anotheraspect, a biomarker is seven or more markers from a metabolic pathwayselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, starch degradation,heme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway. In another aspect, a biomarker is eight or moremarkers from a metabolic pathway selected from the group consisting ofbenzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, starch degradation, heme biosynthesis, lipopolysaccharidebiosynthesis, ubiquinone and other terpenoid quinine biosynthesis,lysine biosynthesis, and oxidative phosphorylation pathway. In anotheraspect, a biomarker is nine or more markers from a metabolic pathwayselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, starch degradation,heme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway. In another aspect, a biomarker is ten or moremarkers from a metabolic pathway selected from the group consisting ofbenzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, starch degradation, heme biosynthesis, lipopolysaccharidebiosynthesis, ubiquinone and other terpenoid quinine biosynthesis,lysine biosynthesis, and oxidative phosphorylation pathway. In anotheraspect, a biomarker is eleven or more markers from a metabolic pathwayselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, starch degradation,heme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway.

In an aspect, this application provides a microbial biomarker and itsuse for selecting a source material with predictive primary outcome oftreatment success in a UC patient. In an aspect, the disclosure providesa microbial taxon, or a subtaxon therein, in a source materialassociated with UC treatment success, where the microbial taxon isselected from the group consisting of Clostridium cluster XVIII,Ruminococcus, Lachnospiraceae, Roseburia inulinivorans, and Eubacteriumhallii.

In an aspect, this application provides a microbial biomarker and itsuse for selecting a source material with predictive primary outcome oftreatment success in a fecal-based therapy in a UC patient. In anotheraspect, the microbial biomarker is a marker from the Roseburia genus. Inanother aspect the microbial biomarker is a Roseburia spp. selected fromthe group consisting of R. inulinivorans, R. cecicola, R. faecis, Rhominis, and R. intestinalis. In another aspect, a microbial biomarkeris Roseburia faecis.

In another aspect, this application provides a microbial biomarker andits use for screening a source material for suitability for a fecalbacteria-based therapy. In an aspect, this application provides amicrobial taxon, or a subtaxon therein, in a source material associatedwith lack of UC treatment success, where the microbial taxon is selectedfrom the group consisting of Fusobacterium, Sutterella, Haemophilus,Escherichia, Megamonas, Clostridium cluster XIVa, Prevotella, Dialister,Veillonella, and Bilophila, or a subtaxon within the microbial taxon. Inanother aspect, this application provide a microbial taxon, or asubtaxon therein, in a source material associated with lack of UCtreatment success, where the microbial taxon is selected from the groupFusobacterium gonidiaformans, Prevotella copri, and Sutterellawadsworthensis.

In another aspect, this application provides a method for selecting asource material for suitability in a fecal bacteria-based therapy basedon the small chain fatty acid content of the material.

In an aspect, a method for selecting a source material for suitabilityin a fecal bacteria-based therapy comprises selecting based on pyruvatefermentation to acetate and lactate. In another aspect, selection isbased on specific bacterial functional pathways associated with primaryoutcome of patients treated with a fecal bacteria-based therapy. Inanother aspect, Benzoate degradation, glycerophospholipid metabolism,secondary bile acid biosynthesis, guanosine penta/tetraphosphatebiosynthesis, pyruvate fermentation to acetate and lactate (short-chainfatty acid biosynthesis), biosynthesis of ansamycins, and starchdegradation are associated with positive primary outcome.

In an aspect, a method for selecting a source material for suitabilityin a fecal bacteria-based therapy comprises selecting based taxacontributing to positive outcomes of patients treated with fecalbacteria-based therapy. In an aspect, source material for fecalbacteria-based therapy is selected from Eubacterium, Ruminococcus,Lachnospiraceae, Roseburia, Dorea, and Coprococcus species. In anotheraspect, source material for fecal bacteria-based therapy is selectedbased on two or more of Eubacterium, Ruminococcus, Lachnospiraceae,Roseburia, Dorea, and Coprococcus species. In another aspect, sourcematerial for fecal bacteria-based therapy is selected based on three ormore of Eubacterium, Ruminococcus, Lachnospiraceae, Roseburia, Dorea,and Coprococcus species. In another aspect, source material for fecalbacteria-based therapy is selected based on three or more ofEubacterium, Ruminococcus, Lachnospiraceae, Roseburia, Dorea, andCoprococcus species. In yet another aspect, source material for fecalbacteria-based therapy is selected based on Eubacterium, Ruminococcus,Lachnospiraceae, Roseburia, Dorea, or Coprococcus species being presentin a source material at a level higher than a predetermined level.

In an aspect, source material for fecal bacteria-based therapy isselected based on levels of taxa selected from the group consisting ofEubacterium hallii, Roseburia inulivorans, Ruminococcus bromii. Inanother aspect, source material is selected based on the levels of oneor more Eubacterium hallii, Roseburia inulivorans, and Ruminococcusbromii, being above a pre-determined level. In another aspect, sourcematerial is selected based on the levels of two or more of Eubacteriumhallii, Roseburia inulivorans, and Ruminococcus bromii, being above apre-determined level. In another aspect, source material is selectedbased on the levels of Eubacterium hallii, Roseburia inulivorans, andRuminococcus bromii, being above a pre-determined level.

In an aspect, this application provides a method for selecting a sourcematerial for suitability in a fecal bacteria-based therapy based on thelevel of Bacteroides in the source material. In an aspect, the level ofBacteroides in a source material selected for use in a fecalbacteria-based therapy is higher than a predetermined level.

In an aspect, this application provides a method for selecting a sourcematerial for suitability in a fecal bacteria-based therapy based on thelevel of Streptococcus species in the source material. In an aspect, thelevel of Streptococcus species in a source material selected for use ina fecal bacteria-based therapy is lower than a predetermined level.

In an aspect, this application provides a metabolic pathway biomarkerand its use for predicting the likelihood of a source material achievinga primary outcome in a patient in need thereof. In another aspect, ametabolic pathway biomarker associated with predictive source materialsuccess is selected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, and starchdegradation.

In an aspect, this application provides a metabolic pathway biomarkerfor predicting treatment failure of a source material when used in afecal bacteria-based therapy. In another aspect, a metabolic pathwaybiomarker associated with UC treatment failure is selected from thegroup consisting of heme biosynthesis, lipopolysaccharide biosynthesis,ubiquinone and other terpenoid quinine biosynthesis, lysine biosynthesisand oxidative phosphorylation pathways. In an aspect, this applicationprovides for selection of a source material for use in a fecalbacteria-based therapy comprising selecting the source material withreduced metabolic pathway biomarkers for predicting treatment failure inpatients.

In an aspect, this application provides a method for selecting a sourcematerial for a fecal bacteria-based therapy based on a reduced presenceof biomarkers shown to indicate a lack of remission (or negative primaryoutcomes) in UC patients. In an aspect, microbial taxa associated withlack of remission are selected from Fusobacterium, Sutterella,Haemophilus, Escherichia, Megamonas, Clostridium XIVa, Prevotalla,Dialister, Veillonella, and Bilophila. In another aspect, Fusobacteriumgonidiaformans and Prevotella OTU2 are associated with lack ofremission. In yet another aspect, Bacteroides uniformis and Bacteroidescoprocola are associated with lack of remission. In a further aspect,Streptococcus species (OTU56) is associated with lack of remission is atreated UC patient. In another aspect, heme biosynthesis is a marker fornegative primary patent outcome.

In an aspect, this disclosure provides a method for treating UC bydecreasing the relative abundance of Bacteroides clarus and/orAkkermansia muciniphila. In an aspect, this disclosure provides a methodfor treating UC by increasing the relative abundance of Faecalibacteriumprausnitzii, Eubacterium rectale, and/or Eubacterium siraeum. In afurther aspect, this disclosure provides a method for treating UC byadministering to a patient a pharmaceutical composition comprising oneor more viable bacteria selected from the group consisting ofFaecalibacterium prausnitzii, Eubacterium rectale, and Eubacteriumsiraeum.

In an aspect, this application provides a pharmaceutical compositioncomprising viable non-pathogenic bacteria from one or more firstmicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans,Eubacterium hallii, and any combination thereof, wherein thepharmaceutical composition contains no bacteria from one or more secondmicrobial taxa selected from the group consisting of Fusobacterium,Sutterella, Haemophilus, Escherichia, Megamonas, Clostridium clusterXIVa, Prevotella, Dialister, Veillonella, and Bilophila.

In another aspect, this application provides a pharmaceuticalcomposition comprising viable non-pathogenic bacteria from one or morefirst microbial taxa selected from the group consisting of Clostridiumcluster XVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans,and Eubacterium hallii, wherein the pharmaceutical composition containsno bacteria from a second microbial taxon selected from the groupconsisting of Fusobacterium gonidiaformans, Prevotella copri, andSutterella wadsworthensis.

In an aspect, this application provides a pharmaceutical compositioncomprising a substantially entire fecal microbiota supplemented,enhanced, or spiked with viable non-pathogenic bacteria from one or moremicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans, andEubacterium hallii.

In an aspect, this application provides a pharmaceutical compositioncomprising a fecal microbe preparation having a relative abundance ratioof 2 or more between a first microbial taxon selected from the groupconsisting of Clostridium cluster XVIII, Ruminococcus, Lachnospiraceae,Roseburia inulinivorans, and Eubacterium hallii, and a second microbialtaxon selected from the group consisting of Fusobacterium, Sutterella,Haemophilus, Escherichia, Megamonas, Clostridium cluster XIVa,Prevotella, Dialister, Veillonella, and Bilophila. In an aspect, asecond microbial taxon is selected from the group consisting ofFusobacterium gonidiaformans, Prevotella copri, and Sutterellawadsworthensis. In another aspect, the relative abundance ratio betweenthe first and second microbial taxa is selected from the groupconsisting of 3 or more, 4 or more, 5 or more, 10 or more, 20 or more,30 or more, 50 or more, 100 or more, and 200 or more.

In an aspect, this application provides a pharmaceutical compositioncomprising a substantially entire fecal microbiota supplemented,enhanced, or spiked with viable non-pathogenic bacteria from a microbialtaxon selected from the group consisting of Bacteroides OTU187,Bacteroides fragilis, and Bacteroides finegoldii.

In an aspect, this application provides a pharmaceutical compositioncomprising viable non-pathogenic bacteria from a first microbial taxonselected from the group consisting of Bacteroides OTU187, Bacteroidesfragilis, and Bacteroides finegoldii. In another aspect, apharmaceutical composition contains no bacteria from a second microbialtaxon selected from the group consisting of Fusobacteriumgonidiaformans, Prevotella copri, and Sutterella wadsworthensis. In afurther aspect, a pharmaceutical composition contains no bacteria from asecond microbial taxon selected from the group consisting of Clostridiumcluster XIVa (OTU173), Streptococcus (OTU56), Sutterella wadsworthensis,Bacteroides uniformis, and Bacteroides coprocola.

In an aspect, this application provides a pharmaceutical compositioncomprising viable non-pathogenic bacteria from the Roseburia spp. Inanother aspect, a pharmaceutical composition comprises viablenon-pathogenic bacteria selected from the group consisting of R.inulinivorans, R. cecicola, R. faecis, R. hominis, and R. intestinalis.In another aspect, a pharmaceutical composition comprises viablenon-pathogenic Roseburia faecis.

In an aspect, this application provides a pharmaceutical compositioncomprising viable non-pathogenic bacteria from one or more firstmicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinovorans,Eubacterium hallii, and any combination thereof, wherein thepharmaceutical composition contains no bacteria from one or more secondmicrobial taxa selected from the group consisting of Fusobacterium,Sutterella, Haemophilus, Escherichia, Megamonas, Clostridium clusterXIVa, Prevotella, Dialister, Veillonella, and Bilophila.

In an aspect, this application provides a pharmaceutical compositioncomprising viable non-pathogenic bacteria from one or more firstmicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia faecis, Eubacteriumhallii, and any combination thereof, wherein the pharmaceuticalcomposition contains no bacteria from one or more second microbial taxaselected from the group consisting of Fusobacterium, Sutterella,Haemophilus, Escherichia, Megamonas, Clostridium cluster XIVa,Prevotella, Dialister, Veillonella, and Bilophila.

In an aspect, this application provides a pharmaceutical compositioncomprising a substantially entire fecal microbiota supplemented,enhanced, or spiked with viable non-pathogenic bacteria from one or moremicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans, andEubacterium hallii.

In an aspect, this application provides a pharmaceutical compositioncomprising a substantially entire fecal microbiota supplemented,enhanced, or spiked with viable non-pathogenic bacteria from one or moremicrobial taxa selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia faecis, and Eubacteriumhallii.

In an aspect, a pharmaceutical composition comprises viablenon-pathogenic bacteria or a fecal microbe preparation from a syntheticculture.

In an aspect, this application provides a pharmaceutical compositioncomprising a fecal microbiota preparation having a suppressed,decreased, reduced, minimized, or undetectable level of a microbialtaxon selected from the group consisting of Clostridium cluster XIVa(OTU173), Streptococcus (OTU56), Sutterella wadsworthensis, Bacteroidesuniformis, and Bacteroides coprocola. In an aspect, a microbial taxon issuppressed or decreased relative to the level of that taxon in a controlfecal microbiota preparation. In an aspect, a microbial taxon issuppressed or decreased relative to the level of that taxon in a healthyadult donor fecal material. In an aspect, a microbial taxon issuppressed or decreased in a treated fecal donor-derived microbepreparation relative to the untreated source fecal material from thefecal donor. In another aspect, an antibiotic specific to a taxon or aheat, ethanol, or chloroform-based treatment is used to suppress ordecrease that taxon. In an aspect, a fecal donor is screened for areduced, minimized, or undetectable level of a microbial taxon mentionedin this paragraph. In another aspect, a synthetic fecal composition isprovided with a lower level of a microbial taxon selected from the groupconsisting of Clostridium cluster XIVa (OTU173), Streptococcus (OTU56),Sutterella wadsworthensis, Bacteroides uniformis, and Bacteroidescoprocola, relative to a fecal microbiota prepared from a healthy adultdonor fecal material.

In an aspect, this application provides a method for treating ulcerativecolitis (UC) in a patient in need thereof, the method comprisingadministering to the patient a pharmaceutical composition describedhere.

In an aspect, this application provides a method for modulating ametabolic marker from a pathway selected from the group consisting ofbenzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, and starch degradation, in a UC patient in need thereof, themethod comprising administering to the patient a pharmaceuticalcomposition described here.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering to the patient amodulator of a metabolic pathway selected from the group consisting ofbenzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, starch degradation, and any combination thereof. In anaspect, a modulator comprises a pharmaceutical composition describedhere. In another aspect, a method comprises upregulating or promotingthe metabolic pathway in a patient's fecal microbiome.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient ispretested for one or more markers from a metabolic pathway selected fromthe group consisting of benzoate degradation, glycerophospholipidmetabolism, secondary bile acid biosynthesis, ppGpp biosynthesis,pyruvate fermentation to acetate and lactate, short chain fatty acidbiosynthesis, biosynthesis of ansamycins, starch degradation, hemebiosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient ispretested for the relative abundance of Fusobacterium gonidiaformans,Prevotella copri, or Sutterella wadsworthensis.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient comprisesa relative abundance of Fusobacterium gonidiaformans, Prevotella copri,or Sutterella wadsworthensis below a pre-determined highest limit.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient comprisesa relative abundance of one or more microbial taxa selected from thegroup consisting of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila, below a pre-determined highest limit.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient comprisesone or more markers, above a pre-determined lowest level, from ametabolic pathway selected from the group consisting of benzoatedegradation, glycerophospholipid metabolism, secondary bile acidbiosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetate andlactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, and starch degradation.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering a pharmaceuticalcomposition disclosed here to the patient, wherein the patient comprisesone or more markers, below a pre-determined highest level, from ametabolic pathway selected from the group consisting of hemebiosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway.

In an aspect, this application provides a method for modulating a markerfrom a pathway selected from the group consisting of heme biosynthesis,lipopolysaccharide biosynthesis, ubiquinone and other terpenoid quininebiosynthesis, lysine biosynthesis, and oxidative phosphorylationpathway, in a UC patient in need thereof, the method comprisingadministering to the patient a pharmaceutical composition disclosedhere.

In an aspect of this disclosure, one or more markers are metabolicmarkers. In another aspect, one or more markers comprise one or moremetabolic pathway genes.

In an aspect, this application provides a method for treating UC in apatient in need thereof, comprising administering to the patient amodulator of a metabolic pathway selected from the group consisting ofheme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, oxidativephosphorylation pathway, and any combination thereof

In an aspect, a modulator comprises a pharmaceutical compositiondisclosed here. In another aspect, a method comprises downregulating orsuppressing the metabolic pathway in the patient's fecal microbiome.

In an aspect, this application provides a method for producing apharmaceutical composition, the method comprising: a) determining in acandidate fecal microbe source material the relative abundance of one ormore bacterial markers selected from the group consisting of BacteroidesOTU187, Bacteroides fragilis, Bacteroides finegoldii, Clostridiumcluster XIVa (OTU173), Streptococcus (OTU56), Sutterella wadsworthensis,Bacteroides uniformis, and Bacteroides coprocola; b) selecting thecandidate fecal microbe source material if the relative abundance ofBacteroides OTU187, Bacteroides fragilis, or Bacteroides finegoldii isabove a pre-determined lowest limit, and/or if the relative abundance ofClostridium cluster XIVa (OTU173), Streptococcus (OTU56), Sutterellawadsworthensis, Bacteroides uniformis, or Bacteroides coprocola is belowa pre-determined highest limit; and c) producing a pharmaceuticalcomposition from the selected fecal microbe source material. In anotheraspect, a pharmaceutical composition is produced for treating UC.

In an aspect, this application provides a method for selecting a fecaldonor, the method comprising: a) determining in a candidate fecal donorthe relative fecal abundance of one or more bacterial markers selectedfrom the group consisting of Bacteroides OTU187, Bacteroides fragilis,Bacteroides finegoldii, Clostridium cluster XIVa (OTU173), Streptococcus(OTU56), Sutterella wadsworthensis, Bacteroides uniformis, andBacteroides coprocola; and b) selecting the candidate fecal donor forfuture fecal donation, if the relative fecal abundance of BacteroidesOTU187, Bacteroides fragilis, or Bacteroides finegoldii is above apre-determined lowest limit, and/or if the relative fecal abundance ofClostridium cluster XIVa (OTU173), Streptococcus (OTU56), Sutterellawadsworthensis, Bacteroides uniformis, or Bacteroides coprocola is belowa pre-determined highest limit. In another aspect, a donor is selectedfor producing a pharmaceutical composition for treating UC.

In an aspect, this application provides a method for selecting a fecalmicrobe source material, the method comprising: a) determining in acandidate fecal microbe source material the relative abundance of one ormore markers from a metabolic pathway selected from the group consistingof fatty acid biosynthesis, propanoate metabolism, secondary bile acidbiosynthesis, glycerophospholipid metabolism, and biosynthesis ofansamycins; and b) selecting the candidate fecal microbe source materialif the relative abundance of the one or more markers is above apre-determined lowest limit.

In an aspect, this application provides a method for selecting a fecalmicrobe source material, the method comprising a.) determining in acandidate fecal microbe source material the relative abundance of one ormore markers from a metabolic pathway selected from the group consistingof fatty acid biosynthesis, propanoate metabolism, secondary bile acidbiosynthesis, glycerophospholipid metabolism, biosynthesis ofansamycins, terpenoid backbone biosynthesis, bacterial chemotaxis, hemebiosynthesis, and short chain fatty acid (SCFA) biosynthesis; and b.)selecting a candidate fecal microbe source material based on therelative abundance of one or more markers.

In an aspect, this application provides a method for selecting a fecalmicrobe source material, the method comprising: a) determining in acandidate fecal microbe source material the relative abundance of one ormore markers from a metabolic pathway selected from the group consistingof terpenoid backbone biosynthesis, bacterial chemotaxis, and hemebiosynthesis; and b) selecting the candidate fecal microbe sourcematerial if the relative abundance of the one or more markers is below apre-determined highest limit.

In another aspect, a fecal microbe source material is selected forproducing a pharmaceutical composition for treating UC. In anotheraspect, one or more markers are metabolic markers. In another aspect,one or more markers comprise one or more metabolic pathway genes.

In an aspect, this application provides a method for selecting a UCpatient for a fecal microbe-based therapy, the method comprising: a)determining in a UC patient one or more markers for the relative fecalabundance of a taxon selected from the group consisting of Clostridiumcluster XVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans,Eubacterium hallii, Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila; and b)selecting the UC patient for a fecal microbe-basedtherapy, if the relative fecal abundance of Clostridium cluster XVIII,Ruminococcus, Lachnospiraceae, Roseburia inulinivorans, or Eubacteriumhallii is above a pre-determined lowest limit, and/or if the relativefecal abundance of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,or Bilophila is below a pre-determined highest limit.

In an aspect, this application provides a method for selecting a UCpatient for a fecal microbe-based therapy, the method comprising: a)determining in a UC patient one or more markers for the relative fecalabundance of a taxon selected from the group consisting of Fusobacteriumgonidiaformans, Prevotella copri, and Sutterella wadsworthensis; and b)selecting the UC patient for a fecal microbe-based therapy, if therelative fecal abundance of the taxon is below a pre-determined highestlimit.

In an aspect, this application provides a method for selecting a UCpatient for a fecal microbe-based therapy, the method comprising: a)determining in a UC patient the relative fecal abundance of one or moremarkers for a metabolic pathway selected from the group consisting ofbenzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, and starch degradation; and b) selecting the UC patient fora fecal microbe-based therapy, if the relative fecal abundance is abovea pre-determined lowest limit.

In an aspect, this application provides a method for selecting a UCpatient for a fecal microbe-based therapy, the method comprising: a)determining in a UC patient the relative fecal abundance of one or moremarkers for a metabolic pathway selected from the group consisting ofheme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway; and b) selecting the UC patient for a fecalmicrobe-based therapy, if the relative fecal abundance is below apre-determined highest limit.

In another aspect, a method for selecting a UC patient further comprisessubjecting a selected UC patient to a fecal microbe-based therapy.

In an aspect, a UC patient of the present disclosure exhibits a Mayoscore of at least 4 prior to treatment, such as a Mayo score of 4, 5, 6,7, 8, 9, 10. In an aspect, a UC patient of the present disclosureexhibits a Mayo score of 4 to 10 prior to treatment, such as 4 to 9, 5to 10, 5 to 8, or 6 to 8.

In an aspect, a UC patient of the present disclosure exhibits an UCEISscore of at least 4 prior to treatment, such as an UCEIS score of 4, 5,6, 7, 8, 9, 10. In an aspect, a UC patient of the present disclosureexhibits a UCEIS score of 4 to 10 prior to treatment, such as 4 to 9, 5to 10, 5 to 8, or 6 to 8.

In an aspect, a UC patient of the present disclosure is capable ofachieving a primary outcome at the end of a treatment regimen, where theprimary outcome is defined as a steroid-free clinical remission andendoscopic remission or response at the end of the treatment regimen,where the steroid free clinical remission is defined as a total Mayoscore of 2 or lower with sub-scores of 1 or lower, and where theendoscopic remission or response is defined as a reduction of at least 1point from baseline in endoscopy score. In another aspect, a UC patientof the present disclosure is capable of achieving a primary outcome atthe end of a treatment regimen, where the primary outcome is defined asa steroid-free clinical remission which is defined as a total Mayo scoreof 2 or lower with sub-scores of 1 or lower. In a further aspect, a UCpatient of the present disclosure is capable of achieving a primaryoutcome at the end of a treatment regimen, where the primary outcome isdefined as a steroid-free endoscopic remission or response which isdefined as a reduction of at least 1 point from baseline in endoscopyscore.

In an aspect, a patient of the present disclosure has no steroid usewithin at least one week prior to commencing the methods providedherein. In another aspect, a patient of the present disclosure has nosteroid use within at least two, three, four, or five weeks prior tocommencing the methods provided herein. In a further aspect, a patientof the present disclosure has no steroid use within at least 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 days prior to commencing themethods provided herein. In an aspect, a steroid may be prednisone,budesonide, or hydrocortisone. In an aspect, a patient of the presentdisclosure has no corticosteroid use within at least one week prior tocommencing the methods provided herein. In an aspect, a patient of thepresent disclosure has no corticosteroid use prior to commencing themethods provided herein.

In an aspect, a method of the present disclosure further comprisedetermining the patient's baseline gut bacterial diversity. In anaspect, a patient's baseline gut bacterial diversity is assessed byanalyzing Shannon's diversity of the patient's fecal sample prior to thetreating step. In an aspect, a patient's baseline fecal Shannondiversity is between 0.5 and 2.2 based on bacterial species level, suchas between 0.5 and 2.0, between 1.0 and 2.2, or between 1.0 and 1.5. Inan aspect, a patient's fecal Shannon diversity increases by at least50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5%, 99.8%, or 99.9% comparedto before treatment. In an aspect, a patient's fecal Shannon diversityincreases by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 20, or 30folds compared to before treatment. In an aspect, a patient'spost-treatment fecal Shannon diversity is between 1.5 and 6.0 based onbacterial species level, such as between 1.5 and 5.0, between 1.5 and4.5, between 1.5 and 4.0, between 1.5 and 3.5, between 1.5 and 3.0,between 1.5 and 2.5, between 1.5 and 2.0, between 2.0 and 4.5, between2.5 and 4.0, between 3.0 and 3.5, between 2.0 and 6.0, between 2.5 and6.0, between 3.0 and 6.0, between 3.5 and 6.0, between 4.0 and 6.0,between 4.5 and 6.0, between 5.0 and 6.0, and between 5.5 and 6.0.

In an aspect, the present disclosure provides a UC treatment that iscapable of achieving a primary outcome rate of at least two fold higherrelative to a primary outcome rate from placebo, where the primaryoutcome is defined as a steroid-free clinical remission and endoscopicremission or response at the end of the UC treatment, where the clinicalremission is defined as a total Mayo score of 2 or lower with allsub-scores of 1 or lower, and where the endoscopic remission or responseis defined as a reduction of at least 1 point from baseline in Mayoendoscopy score. In an aspect, the present disclosure provides a UCtreatment that is capable of achieving a primary outcome rate higherthan a primary outcome rate from placebo, where the primary outcome isdefined as a steroid-free clinical remission and endoscopic remission orresponse at the end of the UC treatment, where the clinical remission isdefined as a total Mayo score of 2 or lower with all sub-scores of 1 orlower, and where the endoscopic remission or response is defined as areduction of at least 1 point from baseline in Mayo endoscopy score.

In an aspect, a UC treatment in accordance with the present disclosureis capable of achieving a primary outcome rate of at least 25%, such asat least 20%, at least 35%, at least 40%, at least 45%, at least 50%, atleast 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, at least 95%, at least 98%, atleast 99%, at least 99.5%, or at least 99.9%. In an aspect, a UCtreatment is capable of achieving a primary outcome rate of between 20%to 40%, such as between 20% and 35%, between 25% and 40%, between 25%and 35%, between 25% and 30%, or between 30% and 35%.

In an aspect, a UC treatment in accordance with the present disclosureis capable of achieving a clinical remission sustaining rate of at least40% at 8 weeks after the completion of the UC treatment. In an aspect, aUC treatment is capable of achieving a clinical remission sustainingrate of at least 45%, such as at least 50%, at least 55%, at least 60%,at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, orat least 99.9% at 8 weeks after the completion of the UC treatment. Inan aspect, a UC treatment is capable of achieving a clinical remissionsustaining rate of between 35% and 60%, such as between 35% and 55%,between 40% and 60%, between 40% and 55%, between 40% and 50%, between45% and 55%, or between 45% and 50% at 8 weeks after the completion ofthe UC treatment.

In an aspect, a UC treatment in accordance with the present disclosureis capable of achieving a steroid-free clinical remission rate of atleast two fold higher relative to a steroid-free clinical remission ratefrom placebo, where the clinical remission is defined as a combined Mayoscore of 1 or lower for rectal bleeding and stool frequency. In anaspect, a UC treatment in accordance with the present disclosure iscapable of achieving a steroid-free clinical remission rate higher thana steroid-free clinical remission rate from placebo, where the clinicalremission is defined as a combined Mayo score of 1 or lower for rectalbleeding and stool frequency. In an aspect, a UC treatment is capable ofachieving a steroid-free clinical remission rate of at least 40%, suchas at least 45%, at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 98%, at least 99%, at least 99.5%, or at least99.9%. In an aspect, a UC treatment is capable of achieving asteroid-free clinical remission rate of between 35% and 55%, such asbetween 40% and 55%, between 35% and 50%, between 40% and 50%, between40% and 45%, or between 45% and 50%.

In an aspect, a UC treatment in accordance with the present disclosureis capable of achieving a steroid-free clinical response rate of atleast two fold higher relative to a steroid-free clinical response ratefrom placebo, where the clinical response is defined as a total Mayoscore decrease of 3 or higher or a 50% higher reduction from baseline incombined score for rectal bleeding and stool frequency. In an aspect, aUC treatment in accordance with the present disclosure is capable ofachieving a steroid-free clinical response rate higher than asteroid-free clinical response rate from placebo, where the clinicalresponse is defined as a total Mayo score decrease of 3 or higher or a50% higher reduction from baseline in combined score for rectal bleedingand stool frequency. In an aspect, a UC treatment is capable ofachieving a steroid-free clinical response rate of at least 50%, such asat least 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, at least 95%, at least 98%, atleast 99%, at least 99.5%, or at least 99.9%. In an aspect, a UCtreatment in accordance with the present disclosure is capable ofachieving a steroid-free clinical response rate between 45% and 65%,such as between 45% and 60%, between 50% and 65%, between 50% and 60%,between 50% and 55%, or between 55% and 60%.

In an aspect, a UC treatment in accordance with the present disclosureis capable of achieving an endoscopic response rate of at least two foldhigher relative to an endoscopic response rate from placebo, where theendoscopic response is defined as a total UCEIS score decrease of 3 orhigher or a 50% or higher reduction from baseline. In an aspect, a UCtreatment in accordance with the present disclosure is capable ofachieving an endoscopic response rate higher than an endoscopic responserate from placebo, where the endoscopic response is defined as a totalUCEIS score decrease of 3 or higher or a 50% or higher reduction frombaseline. In an aspect, a UC treatment is capable of achieving anendoscopic rate of at least 30%, such as at least 35%, at least 40%, atleast 45%, at least 50%, at least 55%, at least 60%, at least 65%, atleast 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 98%, at least 99%, at least 99.5%, or at least99.9%. In an aspect, a UC treatment is capable of achieving anendoscopic response rate between 30% and 45%, such as between 30% and40%, between 35% and 45%, or between 35% and 40%.

In an aspect, the present disclosure provides a method for treatingulcerative colitis in a patient in need thereof, where the methodcomprises administering to a UC patient a pharmaceutically active doseof a pharmaceutical composition comprising viable non-pathogenic fecalbacteria described here. In another aspect, this disclosure provides useof a composition comprising viable non-pathogenic fecal bacteria in themanufacture of a medication for the treatment of ulcerative colitis.

In an aspect, a method of the present disclosure treats a form ofulcerative colitis selected from the group consisting of ulcerativeproctitis, proctosigmoiditis, left-sided colitis, and pan-ulcerativecolitis. In an aspect, a pharmaceutical composition in accordance withthe present disclosure comprises a fecal microbiota preparation. In anaspect, a pharmaceutical composition comprises an isolated or purifiedpopulation of viable non-pathogenic fecal bacteria. In an aspect, apharmaceutical composition comprises a non-selective fecal microbiota.In an aspect, a pharmaceutical composition comprises a non-selected andsubstantially complete fecal microbiota. In another aspect, apharmaceutical composition comprises a substantially complete fecalmicrobiota. In an aspect, a method further comprises administering a5-aminosalicylic acid agent, a corticosteroid, an immunosuppressant, ora combination thereof. In another aspect, a method further comprisesadministering 5-aminosalicylic acid or a derivative thereof,sulfasalazine or a derivative thereof, or a combination thereof

In an aspect, the present disclosure provides a method for selecting atreatment plan for treating ulcerative colitis in a patient in needthereof, where the method comprises determining the level ofFusobacterium gonidiaformans, Prevotella copri, and/or Sutterellawadsworthensis in the patient's gut; and recommending a fecalbacteria-based therapy when the level of Fusobacterium gonidiaformans,Prevotella copri, and/or Sutterella wadsworthensis is above apredetermined level. In an aspect, the level of Fusobacteriumgonidiaformans, Prevotella copri, and/or Sutterella wadsworthensis isabout 8% above a predetermined level, such as about 10%, about 15%,about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%,about 85%, about 90%, about 95%, about 100%, about 150%, or about 200%above a predetermined level. In an aspect, the present disclosureprovides a method for selecting a treatment plan for treating ulcerativecolitis in a patient in need thereof, where the method comprisesdetermining the level of Fusobacterium gonidiaformans, Prevotella copri,and/or Sutterella wadsworthensis in the patient's gut; and recommendinga fecal bacteria-based therapy when the level of Fusobacteriumgonidiaformans, Prevotella copri, and/or Sutterella wadsworthensis isbetween a predetermined range. In an aspect, the predetermined range isabout 8% to about 50% above a predetermined level, such as about 8% toabout 40%, about 10% to 50%, about 15% to about 40%, about 20% to about35%, or about 25% to about 30% above a predetermined level. In anaspect, the predetermined range is about 50% to about 200% above apredetermined level, such as about 50% to about 150%, about 50% to about100%, about 100% to 150%, about 80% to about 120%, about 90% to about110%, or about 98% to about 100% above a predetermined level. In anaspect, the level of one or more bacteria is determined via analyzing apatient's feces.

In an aspect, the present disclosure provides a method for selecting atreatment plan for treating ulcerative colitis in a patient in needthereof, where the method comprises determining the level of one or morebacteria selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans, andEubacterium hallii in the patient's gut; and recommending a fecalbacteria-based therapy when the level of the one or more selectedbacteria is above a predetermined level. In an aspect, the level of theone or more selected bacteria is about 8% above a predetermined level,such as about 10%, about 15%, about 20%, about 25%, about 30%, about35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%,about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about100%, about 150%, or about 200% above a predetermined level. In anaspect, the present disclosure provides a method for selecting atreatment plan for treating ulcerative colitis in a patient in needthereof, where the method comprises determining the level of one or morebacteria selected from the group consisting of Clostridium clusterXVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans, andEubacterium hallii in the patient's gut; and recommending a fecalbacteria-based therapy when the level of the one or more selectedbacteria is between a predetermined range. In an aspect, thepredetermined range is about 8% to about 50% above a predeterminedlevel, such as about 8% to about 40%, about 10% to 50%, about 15% toabout 40%, about 20% to about 35%, or about 25% to about 30% above apredetermined level. In an aspect, the predetermined range is about 50%to about 200% above a predetermined level, such as about 50% to about150%, about 50% to about 100%, about 100% to 150%, about 80% to about120%, about 90% to about 110%, or about 98% to about 100% above apredetermined level. In an aspect, the level of one or more bacteria isdetermined via analyzing a patient's feces.

In an aspect, a predetermined level, a predetermined highest limit, or apredetermined lowest limit is established by the corresponding level ofthe one or more selected bacteria in healthy subjects. In an aspect, apredetermined level, a predetermined highest limit, or a predeterminedlowest limit is established by the corresponding level of the one ormore selected bacteria in healthy subjects in the same demographiccategory as the subject. In an aspect, a predetermined level, apredetermined highest limit, or a predetermined lowest limit isestablished by the abundance of the total Clostridium or Bacteriodetespopulation in the same subject.

In an aspect, the present disclosure provides a method which eliminatesor reduces one or more ulcerative colitis symptoms selected from thegroup consisting of diarrhea, cramp, tenesmus, weight loss, bleeding,loss of appetite, abdominal pain, fever, fatigue, anaemia, inflammation,and micro-ulcers.

In an aspect, the present disclosure provides a method for treatingulcerative colitis in a patient in need thereof, where the methodcomprises administering to a UC patient a pharmaceutically active doseof a pharmaceutical composition comprising viable non-pathogenicbacteria described here. In an aspect, the present disclosure provides amethod for treating ulcerative colitis in a patient in need thereof,where the method comprises administering daily to a UC patient apharmaceutically active dose of a pharmaceutical composition comprisingviable non-pathogenic fecal bacteria. In an aspect, a pharmaceuticalcomposition is administered to an ulcerative colitis patient in needthereof at least once daily for at least two consecutive days. In anaspect, a pharmaceutical composition is administered at least once dailyfor at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutivedays. In another aspect, a pharmaceutical composition is administered atleast once daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12consecutive weeks. In an aspect, a pharmaceutical composition isadministered at least once daily for at most 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive days or weeks. Inanother aspect, a pharmaceutical composition is administered at leastonce daily for at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12consecutive weeks or months. In a further aspect, a pharmaceuticalcomposition is administered at least once for at least 1, 2, 3, 4, 5, 6,7, 8, 9, 10, 11, or 12 consecutive months or years, chronically for apatient's entire life span, or an indefinite period of time.

In an aspect, a pharmaceutical composition is administered to anulcerative colitis patient in need thereof at least twice daily for atleast two consecutive days. In an aspect, a pharmaceutical compositionis administered at least twice daily for at least 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, or 15 consecutive days. In another aspect, apharmaceutical composition is administered at least twice daily for atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks. In anaspect, a pharmaceutical composition is administered at least twicedaily for at most 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, or 20 consecutive days or week. In another aspect, a pharmaceuticalcomposition is administered at least twice daily for at most 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks or months. In a furtheraspect, a pharmaceutical composition is administered at least twice forat least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months oryears, chronically for a patient's entire life span, or an indefiniteperiod of time.

In an aspect, a pharmaceutical composition is administered to anulcerative colitis patient in need thereof at least three times dailyfor at least two consecutive days. In an aspect, a pharmaceuticalcomposition is administered at least three times daily for at least 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive days. In anotheraspect, a pharmaceutical composition is administered at least threetimes daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12consecutive weeks. In an aspect, a pharmaceutical composition isadministered at least three times daily for at most 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive days or weeks.In another aspect, a pharmaceutical composition is administered at leastthree times daily for at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12consecutive weeks or months. In a further aspect, a pharmaceuticalcomposition is administered at least three times for at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months or years, chronicallyfor a patient's entire life span, or an indefinite period of time.

In an aspect, the present disclosure provides a method for treatingulcerative colitis in a patient in need thereof, where the methodcomprises administering orally to a UC patient a pharmaceutically activedose of a pharmaceutical composition comprising viable, non-pathogenic,synthetic bacterial mixture or viable, non-pathogenic, purified orextracted, fecal microbiota, where the dose is administered at a dosingschedule of at least once or twice daily for at least three consecutivedays or weeks. In another aspect, a dose is administered at least once,twice, or three times daily for a period between 1 and 12 weeks, between2 and 12 weeks, between 3 and 12 weeks, between 4 and 12 weeks, between5 and 12 weeks, between 6 and 12 weeks, between 7 and 12 weeks, between8 and 12 weeks, between 9 and 12 weeks, between 10 and 12 weeks, between1 and 2 weeks, between 2 and 3 weeks, between 3 and 4 weeks, between 4and 5 weeks, between 5 and 6 weeks, between 6 and 7 weeks, between 7 and8 weeks, between 8 and 9 weeks, between 9 and 10 weeks, or between 10and 11 weeks.

In an aspect, the present disclosure provides a method for treatingulcerative colitis in a patient in need thereof, where the methodcomprises a first dosing schedule followed by a second dosing schedule.In an aspect, a first dosing schedule comprises a treatment or inductiondose. In an aspect, a first dosing schedule comprises a continuousdosing schedule. In another aspect, a second dosing schedule comprises amaintenance dose lower than or equal to a pharmaceutically active doseof a first dosing schedule. In another aspect, a second dosing schedulelasts for at least about 2, 4, 6, 8, 10, 12, 18, 24, 36, 48, 72, or 96months. In an aspect, a second dosing schedule lasts permanently, for atreated patient's entire life span, or an indefinite period of time. Inan aspect, a second dosing schedule is a continuous dosing schedule. Inanother aspect, a second dosing schedule is an intermittent dosingschedule. In a further aspect, a second dosing schedule is anintermittent dosing schedule comprising a treatment period of at least1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 days followed by aresting period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or14 days. In another aspect, a second dosing schedule comprisesadministering a second dose (e.g., a maintenance dose) every other day,every two days, or every 3, 4, 5, 6, 7, 8 days. In another aspect, amaintenance dose is administered for an extended period of time with orwithout titration (or otherwise changing the dosage or dosing schedule).In an aspect, the interval between a first and a second dosing scheduleis at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 weeks. Inanother aspect, a second dosing schedule (e.g., a maintenance dose)comprises a dosage about 2, 5, 10, 50, 100, 200, 400, 800, 1000, 5000 ormore folds lower than the dosage used in a first dosing schedule (e.g.,an initial treatment dose). In another aspect, a second dosing schedule(e.g., a maintenance dosing schedule) has an equal or lower dosingfrequency than a first dosing schedule (e.g., an initial treatmentdosing schedule). In another aspect, a second dosing schedule (e.g., amaintenance dosing schedule) has a higher dosing interval than a firstdosing schedule (e.g., an initial treatment dosing schedule).

In an aspect, a first or second dosing schedule used in a method can beonce-a-week, twice-a-week, or thrice-a-week. The term “once-a-week”means that a dose is administered once in a week, preferably on the sameday of each week. “Twice-a-week” means that a dose is administered twotimes in a week, preferably on the same two days of each weekly period.“Thrice-a-week” means that a dose is administered three times in a week,preferably on the same three days of each weekly period.

In an aspect, a patient being treated is a patient already withulcerative colitis. Administration of a disclosed pharmaceuticalcomposition to a clinically symptomatic human subject who is geneticallypredisposed or prone to ulcerative colitis is also useful in preventingor inhibiting the onset of clinical symptoms of ulcerative colitis. Ahuman subject genetically predisposed or prone to ulcerative colitis canbe a human subject having a close family member or relative exhibitingor having suffered ulcerative colitis. In another aspect, a subjectbeing treated is a subject in which ulcerative colitis is to beprevented or inhibited. In another aspect, a subject being treated ispredisposed or susceptible to ulcerative colitis. In another aspect, apatient being treated is a patient diagnosed as having ulcerativecolitis. In an aspect, a patient being treated is a patient in needthereof

In an aspect, a patient is a male patient. In an aspect, a patient is afemale patient. In an aspect, a patient is a premature newborn. In anaspect, a patient is a term newborn. In an aspect, a patient is aneonate. In an aspect, a patient is an infant. In an aspect, a patientis a toddler. In an aspect, a patient is a young child. In an aspect, apatient is a child. In an aspect, a patient is an adolescent. In anaspect, a patient is a pediatric patient. In an aspect, a patient is ageriatric patient. In an aspect, a human patient is a child patientbelow about 18, 15, 12, 10, 8, 6, 4, 3, 2, or 1 year old. In anotheraspect, a human patient is an adult patient. In another aspect, a humanpatient is an elderly patient. In a further aspect, a human patient is apatient above about 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,or 95 years old. In another aspect, a patient is about between 1 and 5,between 2 and 10, between 3 and 18, between 21 and 50, between 21 and40, between 21 and 30, between 50 and 90, between 60 and 90, between 70and 90, between 60 and 80, or between 65 and 75 years old. In an aspect,a patient is a young old patient (65-74 years). In an aspect, a patientis a middle old patient (75-84 years). In an aspect, a patient is an oldpatient (>85 years).

In an aspect, a method comprises administering a pharmaceuticalcomposition orally, by enema, or via rectal suppository. In an aspect, apharmaceutical composition administered herein is formulated as anenteric coated (and/or acid-resistant) capsule or microcapsule, orformulated as part of or administered together with a food, a foodadditive, a dairy-based product, a soy-based product or a derivativethereof, a jelly, or a yogurt. In another aspect, a pharmaceuticalcomposition administered herein is formulated as an acid-resistantenteric coated capsule. A pharmaceutical composition can be provided asa powder for sale in combination with a food or drink. A food or drinkcan be a dairy-based product or a soy-based product. In another aspect,a food or food supplement contains enteric-coated and/or acid-resistantmicrocapsules containing a pharmaceutical composition.

In an aspect, a pharmaceutical composition comprises a liquid culture.In another aspect, a pharmaceutical composition is lyophilized,pulverized and powdered. It may then be infused, dissolved such as insaline, as an enema. Alternatively the powder may be encapsulated asenteric-coated and/or acid-resistant capsules for oral administration.These capsules may take the form of enteric-coated and/or acid-resistantmicrocapsules. A powder can preferably be provided in a palatable formfor reconstitution for drinking or for reconstitution as a foodadditive. In a further aspect, a food is yogurt. In an aspect, a powdermay be reconstituted to be infused via naso-duodenal infusion.

In another aspect, a pharmaceutical composition administered herein isin a liquid, frozen, freeze-dried, spray-dried, lyophilized, or powderform. In a further aspect, a pharmaceutical composition administeredherein is formulated as a delayed or gradual enteric release form. Inanother aspect, a pharmaceutical composition administered hereincomprises an excipient, a saline, a buffer, a buffering agent, or afluid-glucose-cellobiose agar (RGCA) media. In another aspect, apharmaceutical composition administered herein comprises acryoprotectant. In an aspect, a cryoprotectant comprises polyethyleneglycol, skim milk, erythritol, arabitol, sorbitol, glucose, fructose,alanine, glycine, proline, sucrose, lactose, ribose, trehalose, dimethylsulfoxide (DMSO), glycerol, or a combination thereof

In one aspect, a pharmaceutical composition comprises a lyophilizedformulation further comprising a reducing agent. In certain embodiments,the reducing agent comprises cysteine selected from the group consistingof D-cysteine and L-cysteine. In another aspect, cysteine is at aconcentration of at least about 0.025%. In one aspect, cysteine is at aconcentration of about 0.025%. In another aspect, cysteine is at aconcentration of 0.025%. In another aspect, another reducing agent otherthan cysteine is used in lieu of, or in combination with cysteine. In anaspect, another reducing agent is selected from the group comprisingascorbic acid, sodium ascorbate, thioglycolic acid, sodium sulfite,sodium bisulfate, sodium metabisulfite, potassium metabisulfite,Glutathione, Methionine, thioglycerol, and alpha tocopherol.

In one aspect, cysteine is at a concentration of at least about 0.005%,at least about 0.01%, at least about 0.015%, at least about 0.02%, atleast about 0.025%, at least about 0.03%, at least about 0.035%, atleast about 0.04%, at least about 0.045%, at least about 0.05%, at leastabout 0.055%, at least about 0.06%, at least about 0.065%, at leastabout 0.07%, at least about 0.075%, at least about 0.08%, at least about0.085%, at least about 0.09%, at least about 0.095%, at least about0.1%, at least about 0.12%, at least about 0.14%, at least about 0.16%,at least about 0.18%, at least about 0.2%, at least about 0.25%, atleast about 0.3%, at least about 0.4%, at least about 0.5%, at leastabout 0.6%, at least about 0.7%, at least about 0.8%, at least about0.9%, at least about 1%, at least about 2%, at least about 4%, at leastabout 6%, at least about 8%, at least about 10%, at least about 12%, atleast about 14%, at least about 16%, at least about 18%, at least about20%, at least about 22%, at least about 24%, or at least about 26%.

In one aspect, a therapeutic composition comprises a cryoprotectant. Asused herein, a “cryoprotectant” refers to a substance that is added to aformulation in order to protect an active ingredient during freezing. Inan aspect, a cryoprotectant comprises, consists essentially of, orconsists of polyethylene glycol, skim milk, erythritol, arabitol,sorbitol, glucose, fructose, alanine, glycine, proline, sucrose,lactose, ribose, trehalose, dimethyl sulfoxide (DMSO), glycerol, or acombination thereof. In an aspect of the present disclosure, acryoprotectant can be selected from the group comprising 5% Sucrose; 10%Sucrose; 10% Skim milk; 10% Trehalose with 2.5% sucrose; 5% Trehalosewith 2.5% sucrose; 5% Mannitol; 5% Mannitol with 0.1% Polysorbate 80;10% Mannitol; 10% Mannitol with 0.1% Polysorbate 80; 5% Trehalose; 5%Trehalose with 0.1% Polysorbate 80; 10% Trehalose; and 10% Trehalosewith 0.1% Polysorbate 80.

In another aspect, a therapeutic composition comprises a lyoprotectant.As used herein, a “lyoprotectant” refers to a substance that is added toa formulation in order to protect an active ingredient during the dryingstage of a lyophilization (also known as freeze-drying) process. In oneaspect, the same substance or the same substance combination is used asboth a cryoprotectant and a lyoprotectant. Exemplary lyoprotectantsinclude sugars such as sucrose or trehalose; an amino acid such asmonosodium glutamate or histidine; a methylamine such as betaine; alyotropic salt such as magnesium sulfate; a polyol such as trihydric orhigher sugar alcohols, e.g. glycerin, erythritol, glycerol, arabitol,xylitol, sorbitol, and mannitol; propylene glycol; polyethylene glycol;Pluronics; and combinations thereof. In one aspect, a lyoprotectant is anon-reducing sugar, such as trehalose or sucrose. In one aspect, acryoprotectant or a lyoprotectant consists essentially of, or consistsof, one or more substances mentioned in this paragraph and the paragraphabove.

In one aspect, a cryoprotectant or a lyoprotectant comprise anintracellular agent, e.g., DMSO, Glycerol, or PEG, which penetratesinside the cell preventing the formation of ice crystals that couldresult in membrane rupture. In another aspect, a cryoprotectant or alyoprotectant comprise an extracellular agent, e.g., sucrose, trehalose,or dextrose, which does not penetrate into the cell membrane but acts toimprove the osmotic imbalance that occurs during freezing.

In one aspect, the present disclosure provides a pharmaceuticalcomposition comprising a lyophilized fecal microbe preparationcomprising a lyophilization formulation comprising at least about 12.5%trehalose.

In one aspect, a lyophilization formulation comprises at least about 5%,at least about 7.5%, at least about 10%, at least about 12.5%, at leastabout 13%, at least about 13.5%, at least about 14%, at least about14.5%, at least about 15%, at least about 15.5%, at least about 16%, atleast about 16.5%, at least about 17%, at least about 17.5%, at leastabout 18%, at least about 18.5%, at least about 19%, at least about19.5%, at least about 20%, at least about 22.5%, at least about 25%, atleast about 27.5%, at least about 30%, at least about 32.5%, at leastabout 35%, at least about 37.5%, at least about 40%, at least about42.5%, at least about 45%, at least about 47.5%, at least about 50%, atleast about 52.5%, at least about 55%, at least about 57.5%, or at leastabout 60% of trehalose.

In an aspect, a pharmaceutical composition administered herein furthercomprises an acid suppressant, an antacid, an H2 antagonist, a protonpump inhibitor or a combination thereof. In an aspect, a pharmaceuticalcomposition administered herein is substantially free of non-livingmatter. In another aspect, a pharmaceutical composition administeredherein is substantially free of acellular material selected from thegroup consisting of residual fiber, DNA, viral coat material, andnon-viable material.

The compositions and methods of the present invention may furthercomprise one or more prebiotics.

A prebiotic is a substrate that is selectively used by a hostmicroorganism to produce a health benefit in a subject/patient. Withoutwishing to be bound by theory, prebiotics are added to nutritionallysupplement bacteria in the microbiome and/or in a microbial composition,e.g., to stimulate the growth or activity of one or more strains ofbeneficial bacteria. Additionally, the prebiotics may be added toprevent “shock” to bacterial strains subsequent to their isolation orpurification, freezing, freeze-drying, spray-drying, reconstitution insolution and the like.

Examples of prebiotics include amino acids, ammonium nitrate, amylose,barley mulch, biotin, carbonate, cellulose, chitin, choline,fructooligosaccharides (FOSs), fructose, galactooligosaccharides (GOSs),glucose, glycerol, heteropolysaccharide, histidine, homopolysaccharide,hydroxyapatite, inulin, isomaltulose, lactose, lactulose, maltodextrins,maltose, mannooligosaccharides, tagatose, nitrogen, oligodextrose,oligofructoses, oligofructose-enriched inulin, oligosaccharides, pectin,phosphate salts, phosphorus, polydextroses, polyols, potash, potassium,sodium nitrate, starch, sucrose, sulfur, sun fiber, tagatose, thiamine,trans-galactooligosaccharides, trehalose, vitamins, a water-solublecarbohydrate, and/or xylooligosaccharides (XOSs).

In embodiments, a prebiotic can be added (e.g., in dry or liquid forms)to a microbial composition of the present invention.

Alternately, or additionally, a prebiotic can be included (e.g., in dryor liquid forms) in a distinct pharmaceutical composition which lacks amicrobial composition of the present invention.

A prebiotic may be provided to a subject before, contemporaneously with,and/or after a pharmaceutical composition comprising a microbialcomposition of the present invention is administered, either in apharmaceutical composition comprising the microbial composition or in apharmaceutical composition lacking a microbial composition.

A prebiotic may be provided in a single dose or in multiple doses. Whenprovided as a single composition, the single composition may comprise asingle prebiotic or a mixture of prebiotics. When provided in multiplecompositions, each composition may comprise a single prebiotic or amixture of prebiotics.

As examples, when multiple doses are provided, a first compositioncomprising a prebiotic may include one specific prebiotic, e.g., inulin,and a second composition may include a second specific prebiotic, e.g.,pectin. Alternately, a first composition may include a mixture ofprebiotics, e.g., inulin and pectin and a second composition may includedifferent mixture of prebiotics, e.g., inulin and a FOS. A firstcomposition may include a mixture of prebiotics and a second compositionmay include one specific prebiotic.

The amount of prebiotic provided to a subject/patient and/or included ina composition depends on the specific prebiotic, the specific bacterialstrain of beneficial bacteria, and/or the disease state of thesubject/patient.

In an aspect, a method further comprises pretreating a subject with anantibiotic composition prior to administering a pharmaceutical bacterialor microbiota composition. In an aspect, an antibiotic compositionadministered herein comprises an antibiotic selected from the groupconsisting of rifabutin, clarithromycin, clofazimine, vancomycin,rifampicin, nitroimidazole, chloramphenicol, and a combination thereof.In another aspect, an antibiotic composition administered hereincomprises an antibiotic selected from the group consisting of rifaximin,rifamycin derivative, rifampicin, rifabutin, rifapentine, rifalazil,bicozamycin, aminoglycoside, gentamycin, neomycin, streptomycin,paromomycin, verdamicin, mutamicin, sisomicin, netilmicin, retymicin,kanamycin, aztreonam, aztreonam macrolide, clarithromycin,dirithromycin, roxithromycin, telithromycin, azithromycin, bismuthsubsalicylate, vancomycin, streptomycin, fidaxomicin, amikacin,arbekacin, neomycin, netilmicin, paromomycin, rhodostreptomycin,tobramycin, apramycin, and a combination thereof. In a further aspect, amethod further comprises pretreating a subject with an anti-inflammatorydrug prior to administration of a pharmaceutical bacterial or microbiotacomposition.

In an aspect, a method achieves a remission, cure, response, orresolution rate of ulcerative colitis of at least about 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, or 99%. In an aspect, a treatment method achieves a reductionof ulcerative colitis disease activity index (UCDAI) after 8 weeks oftreatment by more than 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11. In anotheraspect, a treatment method achieves a reduction of ulcerative colitisdisease activity index (UCDAI) after 8 weeks of treatment by more than2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 in at least 10%, 20%, 30%, 50%, 60%,70%, 80%, or 90% patients in a patient population. In an aspect, atreatment method achieves at least 10%, 20%, 30%, 50%, 60%, 70%, 80%, or90% reduction of ulcerative colitis disease activity index (UCDAI) after8 weeks of treatment compared to baseline (e.g., immediately prior totreatment). In an aspect, a treatment method achieves at least 10%, 20%,30%, 50%, 60%, 70%, 80%, or 90% reduction of ulcerative colitis diseaseactivity index (UCDAI) in at least 10%, 20%, 30%, 50%, 60%, 70%, 80%, or90% patients after 8 weeks of treatment compared to baseline (e.g.,immediately prior to treatment).

In a further aspect, a patient is assessed using the Disease ActivityIndex (DAI) or Mayo score system as described in Schroeder et al.,Coated oral 5-aminosalcylic acid therapy for mildly to moderately activeulcerative colitis. N Eng J Med. 1987; 317: 1625-1629. In an aspect, atreatment method achieves at least 10%, 20%, 30%, 50%, 60%, 70%, 80%, or90% reduction of Mayo score after 8 weeks of treatment compared tobaseline (e.g., immediately prior to treatment). In an aspect, atreatment method achieves at least 10%, 20%, 30%, 50%, 60%, 70%, 80%, or90% reduction of Mayo score in at least 10%, 20%, 30%, 50%, 60%, 70%,80%, or 90% patients after 8 weeks of treatment compared to baseline(e.g., immediately prior to treatment).

In an aspect, a pharmaceutically active or therapeutically effectivedose comprises at least about 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹²,or 10¹³ cfu. In another aspect, a pharmaceutically activetherapeutically effective dose comprises at most about 10⁵, 10⁶, 10⁷,10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², or 10¹³ cfu. In a further aspect, apharmacologically active therapeutically effective dose is selected fromthe group consisting of from 10⁸ cfu to 10¹⁴ cfu, from 10⁹ cfu to 10¹³cfu, from 10¹⁰ cfu to 10¹² cfu, from 10⁹ cfu to 10¹⁴ cfu, from 10⁹ cfuto 10¹² cfu, from 10⁹ cfu to 10¹¹ cfu, from 10⁹ cfu to 10¹⁰ cfu, from10¹⁰ cfu to 10¹⁴ cfu, from 10¹⁰ cfu to 10¹³ cfu, from 10¹¹ cfu to 10¹⁴cfu, from 10¹¹ cfu to 10¹³ cfu, from 10¹² cfu to 10¹⁴ cfu, and from 10¹³cfu to 10¹⁴ cfu.

In an aspect, a pharmaceutically active or therapeutically effectivedose comprises at least about 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹²,or 10¹³ cells or spores. In another aspect, a pharmaceutically active ortherapeutically effective dose comprises at most about 10⁵, 10⁶, 10⁷,10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², or 10¹³ total cells or spores. In a furtheraspect, a pharmacologically active or therapeutically effective dose isselected from the group consisting of from 10⁸ to 10¹⁴, from 10⁹ to10¹³, from 10¹⁰ to 10¹², from 10⁹ to 10¹⁴, from 10⁹ to 10¹², from 10⁹ to10¹¹, from 10⁹ to 10¹⁰, from 10¹⁰ to 10¹⁴, from 10¹⁰ to 10¹³, from 10¹¹to 10¹⁴, from 10¹¹ to 10¹³, from 10¹² to 10¹⁴, and from 10¹³ to 10¹⁴cells or spores. In an aspect, the pharmaceutically active ortherapeutically effective dose cell count is directed to viable cells.

In an aspect, a pharmaceutical composition administered herein comprisesa fecal microbiota. In another aspect, the preparation of a fecalmicrobiota used herein involves a treatment selected from the groupconsisting of ethanol treatment, detergent treatment, heat treatment,irradiation, and sonication. In another aspect, the preparation of afecal microbiota used herein involves no treatment selected from thegroup consisting of ethanol treatment, detergent treatment, heattreatment, irradiation, and sonication. In an aspect, the preparation ofa fecal microbiota used herein involves a separation step selected fromthe group consisting of density gradients, filtration (e.g., sieves,nylon mesh), and chromatography. In another aspect, the preparation of afecal microbiota used herein involves no separation step selected fromthe group consisting of density gradients, filtration (e.g., sieves,nylon mesh), and chromatography. In another aspect, a fecal microbiotaused herein comprises a donor's entire fecal microbiota. In anotheraspect, a pharmaceutical composition administered herein comprises afecal microbiota substantially free of eukaryotic cells from the fecalmicrobiota's donor.

In another aspect, a pharmaceutical composition administered hereincomprises a fecal microbiota further supplemented, spiked, or enhancedwith a fecal microorganism. In an aspect, a fecal microbiota issupplemented with a non-pathogenic (or with attenuated pathogenicity)bacterium of Clostridium, Collinsella, Dorea, Ruminococcus, Coprococcus,Prevotella, Veillonella, Bacteroides, Baccillus, or a combinationthereof. In another aspect, a pharmaceutical composition administeredherein comprises a fecal microbiota further supplemented, spiked, orenhanced with a species of Veillonellaceae, Firmicutes,Gammaproteobacteria, Bacteroidetes, or a combination thereof. In anotheraspect, a pharmaceutical composition administered herein comprises afecal microbiota further supplemented with fecal bacterial spores. In anaspect, fecal bacterial spores are Clostridium spores, Bacillus spores,or both.

In a further aspect, a pharmaceutical composition comprises fecalbacteria from at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 differentfamilies. In a further aspect, a pharmaceutical composition comprisesfecal bacteria from multiple donors. In an aspect, a pharmaceuticalcomposition provided or administered herein comprises a fecal microbiotacomprising no greater than 0.05%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%,0.7%, 0.8%, 0.9%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, or 10% weightnon-living material/weight biological material. In another aspect, apharmaceutical composition provided or administered herein comprises afecal microbiota comprising no greater than 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% weightnon-living material/weight biological material. In another aspect, apharmaceutical composition provided or administered herein comprises,consists of, or consists essentially of, particles of non-livingmaterial and/or particles of biological material of a fecal sample thatpasses through a sieve, a column, or a similar filtering device having asieve, exclusion, or particle filter size of 2.0 mm, 1.0 mm, 0.5 mm,0.25 mm, 0.212 mm, 0.180 mm, 0.150 mm, 0.125 mm, 0.106 mm, 0.090 mm,0.075 mm, 0.063 mm, 0.053 mm, 0.045 mm, 0.038 mm, 0.032 mm, 0.025 mm,0.020 mm, 0.01 mm, or 0.2 mm. “Non-living material” does not include anexcipient, e.g., a pharmaceutically inactive substance, such as acryoprotectant, added to a processed fecal material. “Biologicalmaterial” refers to the living material in fecal material, and includesmicrobes including prokaryotic cells, such as bacteria and archaea(e.g., living prokaryotic cells and spores that can sporulate to becomeliving prokaryotic cells), eukaryotic cells such as protozoa and fungi,and viruses. In one embodiment, “biological material” refers to theliving material, e.g., the microbes, eukaryotic cells, and viruses,which are present in the colon of a normal healthy human. In an aspect,a pharmaceutical composition provided or administered herein comprisesan extract of human feces where the composition is substantiallyodorless. In an aspect, a pharmaceutical composition provided oradministered herein comprises fecal material or a fecal floralpreparation in a lyophilized, crude, semi-purified or purifiedformulation.

In an aspect, a fecal microbiota in a pharmaceutical compositioncomprises highly refined or purified fecal flora, e.g., substantiallyfree of non-floral fecal material. In an aspect, a fecal microbiota canbe further processed, e.g., to undergo microfiltration before, after, orbefore and after sieving. In another aspect, a highly purified fecalmicrobiota product is ultra-filtrated to remove large molecules butretain the pharmaceutical microflora, e.g., bacteria.

In another aspect, a fecal microbiota in a pharmaceutical compositionused herein comprises or consists essentially of a substantiallyisolated or a purified fecal flora or entire (or substantially entire)microbiota that is (or comprises) an isolate of fecal flora that is atleast about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%,99.6%, 99.7%, 99.8% or 99.9% isolated or pure, or having no more thanabout 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9% or 1.0% ormore non-fecal floral material; or, a substantially isolated, purified,or substantially entire microbiota as described in Sadowsky et al., WO2012/122478 A1, or as described in Borody et al., WO 2012/016287 A2.

In an aspect, a fecal microbiota in a pharmaceutical compositioncomprises a donor's substantially entire or non-selected fecalmicrobiota, reconstituted fecal material, or synthetic fecal material.In another aspect, the fecal microbiota in a pharmaceutical compositioncomprises no antibiotic resistant population. In another aspect, apharmaceutical composition comprises a fecal microbiota and is largelyfree of extraneous matter (e.g., non-living matter including acellularmatter such as residual fiber, DNA, RNA, viral coat material, non-viablematerial; and living matter such as eukaryotic cells from the fecalmatter's donor).

In an aspect, a fecal microbiota in a pharmaceutical composition usedherein is derived from disease-screened fresh homologous feces orequivalent freeze-dried and reconstituted feces. In an aspect, a freshhomologous feces does not include an antibiotic resistant population. Inanother aspect, a fecal microbiota in a pharmaceutical composition isderived from a synthetic fecal composition. In an aspect, a syntheticfecal composition comprises a preparation of viable flora whichpreferably in proportional content, resembles normal healthy human fecalflora which does not include antibiotic resistant populations. Suitablemicroorganisms may be selected from the following: Bacteroides,Eubacterium, Fusobacterium, Propionibacterium, Lactobacillus,Ruminococcus, Escherichia coli, Gemmiger, Clostridium, Desulfomonas,Peptostreptococcus, Bifidobacterium, Collinsella, Coprococcus, Dorea,and Ruminococcus.

In one aspect, an exemplary therapeutic composition comprises startingmaterial from a donor from a defined donor pool, where this donorcontributes a stool that is centrifuged, then filtered with veryhigh-level filtration using e.g., either metal sieving or Milliporefilters, or equivalent, to ultimately permit only cells of bacterialorigin to remain, e.g., often less than about 5 micrometers diameter.After the initial centrifugation, the solid material is separated fromthe liquid, and the solid is then filtered in progressively reducingsize filters and tangential filters, e.g., using a Millipore filtration,and optionally, also comprising use of nano-membrane filtering. Thefiltering can also be done by sieves as described in WO 2012/122478, butin contrast using sieves that are smaller than 0.0120 mm, down to about0.0110 mm, which ultimately result in having only bacterial cellspresent.

The supernatant separated during centrifugation is now taken andfiltered progressively in a filtering, e.g., a Millipore filtering orequivalent systems, to end up with liquid which is finely filteredthrough an about 0.22 micron filter. This removes all particulate matterincluding all living matter, including bacteria and viruses. The productthen is sterile, but the aim is to remove the bacteria but to keep theirsecretions, especially antimicrobial bacteriocins, bacteria-derivedcytokine-like products and all accompanying Biologically ActiveMolecules (BAMs), including: thuricin (which is secreted by bacilli indonor stools), bacteriocins (including colicin, troudulixine orputaindicine, or microcin or subtilosin A), lanbiotics (including nisin,subtilin, epidermin, mutacin, mersacidin, actagardine, cinnamycin),lacticins and other antimicrobial or anti-inflammatory compounds.

In one aspect, a therapeutic composition used here comprises areconstituted fecal flora consisting essentially of a combination of apurified fecal microbiota and a non-cellular fecal filtrate. In anotheraspect, a therapeutic composition used here comprises a purified fecalmicrobiota supplemented with one or more non-cellular non-particulatefecal components. In one aspect, a therapeutic composition used herecomprises one or more non-cellular non-particulate fecal components. Inone aspect, one or more non-cellular non-particulate fecal componentscomprise synthetic molecules, biologically active molecules produced bya fecal microorganism, or both. In another aspect, one or morenon-cellular non-particulate fecal components comprise biologicallyactive proteins or peptides, micronutrients, fats, sugars, smallcarbohydrates, trace elements, mineral salts, ash, mucous, amino acids,nutrients, vitamins, minerals, or any combination thereof. In oneaspect, one or more non-cellular non-particulate fecal componentscomprise one or more biologically active molecules selected from thegroup consisting of bacteriocin, lanbiotic, and lacticin. In anotheraspect, one or more non-cellular non-particulate fecal componentscomprise one or more bacteriocins selected from the group consisting ofcolicin, troudulixine, putaindicine, microcin, and subtilosin A. In oneaspect, one or more non-cellular non-particulate fecal componentscomprise one or more lanbiotics selected from the group consisting ofthuricin, nisin, subtilin, epidermin, mutacin, mersacidin, actagardine,and cinnamycin. In another aspect, one or more non-cellularnon-particulate fecal components comprise an anti-spore compound, anantimicrobial compound, an anti-inflammatory compound, or anycombination thereof. In a further aspect, one or more non-cellularnon-particulate fecal components comprise an interleukin, a cytokine, aleukotriene, an eicosanoid, or any combination thereof

In another aspect, a treatment method provided here comprises the use ofboth fecal bacterial cells, e.g., a partial or a complete representationof the human GI microbiota, and an isolated, processed, filtered,concentrated, reconstituted and/or artificial liquid component (e.g.,fecal filtrate) of the flora (the microbiota) which comprises, amongothers ingredients, bacterial secretory products such as e.g.,bacteriocins (proteinaceous toxins produced by bacteria, includingcolicin, troudulixine or putaindicine, or microcin or subtilosin A),lanbiotics (a class of peptide antibiotics that contain a characteristicpolycyclic thioether amino acid lanthionine or methyllanthionine, andunsaturated amino acids dehydroalanine and 2-aminoisobutyric acid; whichinclude thuricin (which is secreted by bacilli in donor stools), nisin,subtilin, epidermin, mutacin, mersacidin, actagardine, cinnamycin), alacticin (a family of pore-forming peptidic toxins) and otherantimicrobial or anti-inflammatory compounds and/or additionalbiologically active molecules (BAMs) produced by bacteria or othermicroorganisms of the microbiota, and/or which are found in the “liquidcomponent” of a microbiota.

In one aspect, a fecal bacteria-based therapeutic composition is usedconcurrently with a fecal non-cellular filtrate-based therapeuticcomposition. In another aspect, a patient is treated with a first fecalnon-cellular filtrate-based therapeutic composition before being given asecond fecal bacteria-based therapeutic composition, or vice versa. In afurther aspect, a treatment method comprises three steps: first,antibiotic pretreatment to non-selectively remove infectiouspathogen(s); second, a fecal non-cellular filtrate-based treatment stepto further suppress selected infectious pathogen(s); and third, givingthe patient a fecal bacteria-based therapeutic composition tore-establish a functional intestinal microbiome.

In an aspect, a pharmaceutical composition is combined with otheradjuvants such as antacids to dampen bacterial inactivation in thestomach. (e.g., Mylanta, Mucaine, Gastrogel). In another aspect, acidsecretion in the stomach could also be pharmacologically suppressedusing H2-antagonists or proton pump inhibitors. An example H2-antagonistis ranitidine. An example proton pump inhibitor is omeprazole. In anaspect, an acid suppressant is administered prior to administering, orin co-administration with, a pharmaceutical composition.

In an aspect, a pharmaceutical composition is in the form of: an enemacomposition which can be reconstituted with an appropriate diluent;enteric-coated capsules; enteric-coated microcapsules; acid-resistanttablet; acid-resistant capsules; acid-resistant microcapsules; powderfor reconstitution with an appropriate diluent for naso-enteric infusionor colonoscopic infusion; powder for reconstitution with appropriatediluent, flavoring and gastric acid suppression agent for oralingestion; powder for reconstitution with food or drink; or food or foodsupplement comprising enteric-coated and/or acid-resistant microcapsulesof the composition, powder, jelly, or liquid.

In an aspect, a treatment method effects a cure, reduction of thesymptoms, or a percentage reduction of symptoms of ulcerative colitis.The change of flora is preferably as “near-complete” as possible and, inan aspect, the flora is replaced by viable organisms which will crowdout any remaining, original flora. Typically the change in enteric floracomprises introduction of an array of predetermined flora into thegastro-intestinal system, and thus in a preferred form the method oftreatment comprises substantially or completely displacing pathogenicenteric flora in patients requiring such treatment.

In another aspect, a pharmaceutical composition can be provided togetherwith a pharmaceutically acceptable carrier. As used herein, a“pharmaceutically acceptable carrier” refers to a non-toxic solvent,dispersant, excipient, adjuvant, or other material which is mixed with aviable bacterium in order to permit the formation of a pharmaceuticalcomposition, e.g., a dosage form capable of administration to thepatient. A pharmaceutically acceptable carrier can be liquid (e.g.,saline), gel or solid form of diluents, adjuvant, excipients or an acidresistant encapsulated ingredient. Suitable diluents and excipientsinclude pharmaceutical grades of physiological saline, dextrose,glycerol, mannitol, lactose, starch, magnesium stearate, sodiumsaccharin, cellulose, magnesium carbonate, and the like, andcombinations thereof. In another aspect, a pharmaceutical compositionmay contain auxiliary substances such as wetting or emulsifying agents,stabilizing or pH buffering agents. In an aspect, a pharmaceuticalcomposition contains about 1%-5%, 5%-10%, 10%-15%, 15-20%, 20%-25%,25-30%, 30-35%, 40-45%, 50%-55%, 1%-95%, 2%-95%, 5%-95%, 10%-95%,15%-95%, 20%-95%, 25%-95%, 30%-95%, 35%-95%, 40%-95%, 45%-95%, 50%-95%,55%-95%, 60%-95%, 65%-95%, 70%-95%, 45%-95%, 80%-95%, or 85%-95% ofactive ingredient. In an aspect, a pharmaceutical composition containsabout 2%-70%, 5%-60%, 10%-50%, 15%-40%, 20%-30%, 25%-60%, 30%-60%, or35%-60% of active ingredient.

In an aspect, a pharmaceutical composition can be incorporated intotablets, drenches, boluses, capsules or premixes. Formulation of theseactive ingredients into such dosage forms can be accomplished by meansof methods well known in the pharmaceutical formulation arts. See, e.g.,U.S. Pat. No. 4,394,377. Filling gelatin capsules with any desired formof the active ingredients readily produces capsules. If desired, thesematerials can be diluted with an inert powdered diluent, such as sugar,starch, powdered milk, purified crystalline cellulose, or the like toincrease the volume for convenience of filling capsules.

In an aspect, conventional formulation processes can be used to preparetablets containing a pharmaceutical composition. In addition to theactive ingredients, tablets may contain a base, a disintegrator, anabsorbent, a binder, and a lubricant. Typical bases include lactose,sugar, sodium chloride, starch and mannitol. Starch is also a gooddisintegrator as is alginic acid. Surface-active agents such as sodiumlauryl sulfate and dioctyl sodium sulphosuccinate are also sometimesused. Commonly used absorbents include starch and lactose. Magnesiumcarbonate is also useful for oily substances. As a binder there can beused, for example, gelatin, gums, starch, dextrin, polyvinyl pyrrolidoneand various cellulose derivatives. Among the commonly used lubricantsare magnesium stearate, talc, paraffin wax, various metallic soaps, andpolyethylene glycol.

In an aspect, for preparing solid compositions such as tablets, anactive ingredient is mixed with a pharmaceutical carrier, e.g.,conventional tableting ingredients such as corn starch, lactose,sucrose, sorbitol, talc, stearic acid, magnesium stearate, dicalciumphosphate or gums, or other pharmaceutical diluents, e.g. water, to forma solid preformulation composition containing a homogeneous mixture of acomposition of the present invention. When referring to thesepreformulation compositions as homogeneous, it is meant that the activeingredient is dispersed evenly throughout the composition so that thecomposition may be readily subdivided into equally effective unit dosageforms such as tablets, pills and capsules. This solid preformulationcomposition is then subdivided into unit dosage forms of the typedescribed above containing a desired amount of an active ingredient(e.g., at least about 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², or 10¹³cfu). A pharmaceutical composition used herein can be flavored.

In an aspect, a pharmaceutical composition can be a tablet or a pill. Inan aspect, a tablet or a pill can be coated or otherwise compounded toprovide a dosage form affording the advantage of prolonged action. Forexample, a tablet or pill can comprise an inner dosage and an outerdosage component, the latter being in the form of an envelope over theformer. The two components can be separated by an enteric layer whichserves to resist disintegration in the stomach and permits the innercomponent to pass intact into the duodenum or to be delayed in release.A variety of materials can be used for such enteric layers or coatings,such materials including a number of polymeric acids and mixtures ofpolymeric acids with such materials as shellac, cetyl alcohol andcellulose acetate.

In an aspect, a pharmaceutical composition can be a drench. In anaspect, a drench is prepared by choosing a saline-suspended form of apharmaceutical composition. A water-soluble form of one ingredient canbe used in conjunction with a water-insoluble form of the other bypreparing a suspension of one with an aqueous solution of the other.Water-insoluble forms of either active ingredient may be prepared as asuspension or in some physiologically acceptable solvent such aspolyethylene glycol. Suspensions of water-insoluble forms of eitheractive ingredient can be prepared in oils such as peanut, corn, sesameoil or the like; in a glycol such as propylene glycol or a polyethyleneglycol; or in water depending on the solubility of a particular activeingredient. Suitable physiologically acceptable adjuvants may benecessary in order to keep the active ingredients suspended. Adjuvantscan include and be chosen from among the thickeners, such ascarboxymethylcellulose, polyvinyl pyrrolidone, gelatin and thealginates. Surfactants generally will serve to suspend the activeingredients, particularly the fat-soluble propionate-enhancingcompounds. Most useful for making suspensions in liquid nonsolvents arealkylphenol polyethylene oxide adducts, naphthalenesulfonates,alkylbenzene-sulfonates, and the polyoxyethylene sorbitan esters. Inaddition many substances, which affect the hydrophilicity, density andsurface tension of the liquid, can assist in making suspensions inindividual cases. For example, silicone anti-foams, glycols, sorbitol,and sugars can be useful suspending agents.

In an aspect, a pharmaceutical composition comprises at least about 10⁵,10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², or 10¹³ cfu. In another aspect, apharmaceutical composition comprises at most about 10⁵, 10⁶, 10⁷, 10⁸,10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³ or 10¹⁴ cfu.

In another aspect, a pharmaceutical composition comprises at least about10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², or 10¹³ cells. In anotheraspect, a pharmaceutical composition comprises at most about 10⁵, 10⁶,10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³ or 10¹⁴ cells.

In another aspect, a pharmaceutical composition and methods thereofcomprise the following embodiments:

Embodiment 1. A pharmaceutical composition comprising viablenon-pathogenic bacteria from one or more first microbial taxa selectedfrom the group consisting of Clostridium cluster XVIII, Ruminococcus,Lachnospiraceae, Roseburia inulinivorans, Eubacterium hallii, and anycombination thereof, wherein said pharmaceutical composition contains nobacteria from one or more second microbial taxa selected from the groupconsisting of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila.

Embodiment 2. A pharmaceutical composition comprising viablenon-pathogenic bacteria from one or more first microbial taxa selectedfrom the group consisting of Clostridium cluster XVIII, Ruminococcus,Lachnospiraceae, Roseburia inulinivorans, and Eubacterium hallii,wherein said pharmaceutical composition contains no bacteria from asecond microbial taxon selected from the group consisting ofFusobacterium gonidiaformans, Prevotella copri, and Sutterellawadsworthensis.

Embodiment 3. A pharmaceutical composition comprising a substantiallyentire fecal microbiota supplemented, enhanced, or spiked with viablenon-pathogenic bacteria from one or more microbial taxa selected fromthe group consisting of Clostridium cluster XVIII, Ruminococcus,Lachnospiraceae, Roseburia inulinivorans, and Eubacterium hallii.

Embodiment 4. A pharmaceutical composition comprising a fecal microbepreparation having a relative abundance ratio of 2 or more between afirst microbial taxon selected from the group consisting of Clostridiumcluster XVIII, Ruminococcus, Lachnospiraceae, Roseburia inulinivorans,and Eubacterium hallii, and a second microbial taxon selected from thegroup consisting of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila.

Embodiment 5. The pharmaceutical composition of embodiment 4, whereinsaid second microbial taxon is selected from the group consisting ofFusobacterium gonidiaformans, Prevotella copri, and Sutterellawadsworthensis.

Embodiment 6. The pharmaceutical composition of embodiment 4, whereinsaid relative abundance ratio is selected from the group consisting of 3or more, 4 or more, 5 or more, 10 or more, 20 or more, 30 or more, 50 ormore, 100 or more, and 200 or more.

Embodiment 7. A pharmaceutical composition comprising a substantiallyentire fecal microbiota supplemented, enhanced, or spiked with viablenon-pathogenic bacteria from a microbial taxon selected from the groupconsisting of Bacteroides OTU187, Bacteroides fragilis, and Bacteroidesfinegoldii.

Embodiment 8. A pharmaceutical composition comprising viablenon-pathogenic bacteria from a first microbial taxon selected from thegroup consisting of Bacteroides OTU187, Bacteroides fragilis, andBacteroides finegoldii.

Embodiment 9. The pharmaceutical composition of embodiment 8, whereinsaid pharmaceutical composition contains no bacteria from a secondmicrobial taxon selected from the group consisting of Fusobacteriumgonidiaformans, Prevotella copri, and Sutterella wadsworthensis.

Embodiment 10. The pharmaceutical composition of embodiment 8, whereinsaid pharmaceutical composition contains no bacteria from a secondmicrobial taxon selected from the group consisting of Clostridiumcluster XIVa (OTU173), Streptococcus (OTU56), Sutterella wadsworthensis,Bacteroides uniformis, and Bacteroides coprocola.

Embodiment 11. The pharmaceutical composition of any one of thepreceding embodiments, wherein said viable non-pathogenic bacteria orsaid fecal microbe preparation are from a synthetic culture.

Embodiment 12. A pharmaceutical composition comprising a fecalmicrobiota preparation having a suppressed, decreased, reduced,minimized, or undetectable level of a microbial taxon selected from thegroup consisting of Clostridium cluster XIVa (OTU173), Streptococcus(OTU56), Sutterella wadsworthensis, Bacteroides uniformis, andBacteroides coprocola.

Embodiment 13. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition is in an anaerobicpackage or container.

Embodiment 14. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition is in a liquid, frozen,freeze-dried, spray-dried, lyophilized, or powder form.

Embodiment 15. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition comprises an excipient,a saline, a buffer, a buffering agent, or a fluid-glucose-cellobioseagar (RGCA) media.

Embodiment 16. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition is formulated as anenteric coated capsule or microcapsule, an acid-resistant capsule ormicrocapsule, an enteric coated tablet, an acid-resistant tablet, apowder suitable for reconstitution, a naso-duodenal infusion, or fordelivery in the form of an enema or a colonoscopic infusion.

Embodiment 17. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition is formulated as adelayed or gradual enteric release form.

Embodiment 18. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition is administeredtogether with a food, a liquid beverage, a food additive, a dairy-basedproduct, a soy-based product or a derivative thereof, a jelly, or ayogurt.

Embodiment 19. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition comprises acryoprotectant.

Embodiment 20. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition comprises acryoprotectant comprises polyethylene glycol, skim milk, erythritol,arabitol, sorbitol, glucose, fructose, alanine, glycine, proline,sucrose, lactose, ribose, trehalose, dimethyl sulfoxide (DMSO),glycerol, or a combination thereof

Embodiment 21. The pharmaceutical composition of any one of embodiments1 to 12, wherein said pharmaceutical composition further comprises anacid suppressant, an antacid, an H2 antagonist, a proton pump inhibitoror a combination thereof

Embodiment 22. A method for treating ulcerative colitis (UC) in apatient in need thereof, said method comprising administering to saidpatient the pharmaceutical composition of any one of embodiments 1 to21.

Embodiment 23. A method for modulating a metabolic marker from a pathwayselected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, and starchdegradation, in a UC patient in need thereof, said method comprisingadministering to said patient the pharmaceutical composition of any oneof embodiments 1 to 21.

Embodiment 24. A method for treating UC in a patient in need thereof,comprising administering to said patient a modulator of a metabolicpathway selected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, starch degradation,and any combination thereof

Embodiment 25. The method of embodiment 24, wherein said modulatorcomprises the pharmaceutical composition of any one of embodiments 1 to21.

Embodiment 26. The method of embodiment 24, wherein said methodcomprises upregulating or promoting said metabolic pathway in saidpatient's fecal microbiome.

Embodiment 27. A method for treating UC in a patient in need thereof,comprising administering the pharmaceutical composition of any one ofembodiments 1 to 21 to said patient, wherein said patient is pretestedfor one or more markers from a metabolic pathway selected from the groupconsisting of benzoate degradation, glycerophospholipid metabolism,secondary bile acid biosynthesis, ppGpp biosynthesis, pyruvatefermentation to acetate and lactate, short chain fatty acidbiosynthesis, biosynthesis of ansamycins, starch degradation, hemebiosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway.

Embodiment 28. A method for treating UC in a patient in need thereof,comprising administering the pharmaceutical composition of any one ofembodiments 1 to 21 to said patient, wherein said patient is pretestedfor the relative abundance of Fusobacterium gonidiaformans, Prevotellacopri, or Sutterella wadsworthensis.

Embodiment 29. A method for treating UC in a patient in need thereof,comprising administering the pharmaceutical composition of any one ofembodiments 1 to 21 to said patient, wherein said patient comprises arelative abundance of Fusobacterium gonidiaformans, Prevotella copri, orSutterella wadsworthensis below a pre-determined highest limit.

Embodiment 30. A method for treating UC in a patient in need thereof,comprising administering the pharmaceutical composition of any one ofembodiments 1 to 21 to said patient, wherein said patient comprises arelative abundance of one or more microbial taxa selected from the groupconsisting of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila, below a pre-determined highest limit.

Embodiment 31. A method for treating UC in a patient in need thereof,comprising administering the pharmaceutical composition of any one ofembodiments 1 to 21 to said patient, wherein said patient comprises oneor more markers, above a pre-determined lowest level, from a metabolicpathway selected from the group consisting of benzoate degradation,glycerophospholipid metabolism, secondary bile acid biosynthesis, ppGppbiosynthesis, pyruvate fermentation to acetate and lactate, short chainfatty acid biosynthesis, biosynthesis of ansamycins, and starchdegradation.

Embodiment 32. A method for treating UC in a patient in need thereof,comprising administering the pharmaceutical composition of any one ofembodiments 1 to 21 to said patient, wherein said patient comprises oneor more markers, below a pre-determined highest level, from a metabolicpathway selected from the group consisting of heme biosynthesis,lipopolysaccharide biosynthesis, ubiquinone and other terpenoid quininebiosynthesis, lysine biosynthesis, and oxidative phosphorylationpathway.

Embodiment 33. A method for modulating a marker from a pathway selectedfrom the group consisting of heme biosynthesis, lipopolysaccharidebiosynthesis, ubiquinone and other terpenoid quinine biosynthesis,lysine biosynthesis, and oxidative phosphorylation pathway, in a UCpatient in need thereof, said method comprising administering to saidpatient the pharmaceutical composition of any one of embodiments 1 to21.

Embodiment 34. The method of any one of embodiments 27 to 33, whereinsaid one or more markers are metabolic markers.

Embodiment 35. The method of any one of embodiments 27 to 33, whereinsaid one or more markers comprise one or more metabolic pathway genes.

Embodiment 36. A method for treating UC in a patient in need thereof,comprising administering to said patient a modulator of a metabolicpathway selected from the group consisting of heme biosynthesis,lipopolysaccharide biosynthesis, ubiquinone and other terpenoid quininebiosynthesis, lysine biosynthesis, oxidative phosphorylation pathway,and any combination thereof.

Embodiment 37. The method of embodiment 36, wherein said modulatorcomprises the pharmaceutical composition of any one of embodiments 1 to21.

Embodiment 38. The method of embodiment 36, wherein said methodcomprises downregulating or suppressing said metabolic pathway in saidpatient's fecal microbiome.

Embodiment 39. A method for producing a pharmaceutical composition, saidmethod comprising

a) determining in a candidate fecal microbe source material the relativeabundance of one or more bacterial markers selected from the groupconsisting of Bacteroides OTU187, Bacteroides fragilis, Bacteroidesfinegoldii, Clostridium cluster XIVa (OTU173), Streptococcus (OTU56),Sutterella wadsworthensis, Bacteroides uniformis, and Bacteroidescoprocola;b) selecting said candidate fecal microbe source material if therelative abundance of Bacteroides OTU187, Bacteroides fragilis, orBacteroides finegoldii is above a pre-determined lowest limit, and/or ifthe relative abundance of Clostridium cluster XIVa (OTU173),Streptococcus (OTU56), Sutterella wadsworthensis, Bacteroides uniformis,or Bacteroides coprocola is below a pre-determined highest limit; andc) producing a pharmaceutical composition from said selected fecalmicrobe source material.

Embodiment 40. The method of embodiment 39, wherein said pharmaceuticalcomposition is for treating UC.

Embodiment 41. A method for selecting a fecal donor, said methodcomprising

a) determining in a candidate fecal donor the relative fecal abundanceof one or more bacterial markers selected from the group consisting ofBacteroides OTU187, Bacteroides fragilis, Bacteroides finegoldii,Clostridium cluster XIVa (OTU173), Streptococcus (OTU56), Sutterellawadsworthensis, Bacteroides uniformis, and Bacteroides coprocola; andb) selecting said candidate fecal donor for future fecal donation, ifthe relative fecal abundance of Bacteroides OTU187, Bacteroidesfragilis, or Bacteroides finegoldii is above a pre-determined lowestlimit, and/or if the relative fecal abundance of Clostridium clusterXIVa (OTU173), Streptococcus (OTU56), Sutterella wadsworthensis,Bacteroides uniformis, or Bacteroides coprocola is below apre-determined highest limit.

Embodiment 42. The method of embodiment 41, wherein said donor isselected for producing a pharmaceutical composition for treating UC.

Embodiment 43. A method for selecting a fecal microbe source material,said method comprising

a) Determining in a candidate fecal microbe source material the relativeabundance of one or more markers from a metabolic pathway selected fromthe group consisting of fatty acid biosynthesis, propanoate metabolism,secondary bile acid biosynthesis, glycerophospholipid metabolism, andbiosynthesis of ansamycins; andb) selecting said candidate fecal microbe source material if therelative abundance of said one or more markers is above a pre-determinedlowest limit.

Embodiment 44. The method of embodiment 43, wherein said fecal microbesource material is selected for producing a pharmaceutical compositionfor treating UC.

Embodiment 45. The method of embodiment 43, wherein said one or moremarkers are metabolic markers.

Embodiment 46. The method of embodiment 43, wherein said one or moremarkers comprise one or more metabolic pathway genes.

Embodiment 47. A method for selecting a fecal microbe source material,said method comprising

a) determining in a candidate fecal microbe source material the relativeabundance of one or more markers from a metabolic pathway selected fromthe group consisting of terpenoid backbone biosynthesis, bacterialchemotaxis, and heme biosynthesis; andb) selecting said candidate fecal microbe source material if therelative abundance of said one or more markers is below a pre-determinedhighest limit.

Embodiment 48. The method of embodiment 47, wherein said fecal microbesource material is selected for producing a pharmaceutical compositionfor treating UC.

Embodiment 49. The method of embodiment 47, wherein said one or moremarkers are metabolic markers.

Embodiment 50. The method of embodiment 47, wherein said one or moremarkers comprise one or more metabolic pathway genes.

Embodiment 51. A method for selecting a UC patient for a fecalmicrobe-based therapy, said method comprising

a) determining in a UC patient one or more markers for the relativefecal abundance of a taxon selected from the group consisting ofClostridium cluster XVIII, Ruminococcus, Lachnospiraceae, Roseburiainulinivorans, Eubacterium hallii, Fusobacterium, Sutterella,Haemophilus, Escherichia, Megamonas, Clostridium cluster XIVa,Prevotella, Dialister, Veillonella, and Bilophila; andb) selecting said UC patient for a fecal microbe-based therapy, if therelative fecal abundance of Clostridium cluster XVIII, Ruminococcus,Lachnospiraceae, Roseburia inulinivorans, or Eubacterium hallii is abovea pre-determined lowest limit, and/or if the relative fecal abundance ofFusobacterium, Sutterella, Haemophilus, Escherichia, Megamonas,Clostridium cluster XIVa, Prevotella, Dialister, Veillonella, orBilophila is below a pre-determined highest limit.

Embodiment 52. A method for selecting a UC patient for a fecalmicrobe-based therapy, said method comprising

a) determining in a UC patient one or more markers for the relativefecal abundance of a taxon selected from the group consisting ofFusobacterium gonidiaformans, Prevotella copri, and Sutterellawadsworthensis; andb) selecting said UC patient for a fecal microbe-based therapy, if therelative fecal abundance of said taxon is below a pre-determined highestlimit.

Embodiment 53. A method for selecting a UC patient for a fecalmicrobe-based therapy, said method comprising

a) determining in a UC patient the relative fecal abundance of one ormore markers for a metabolic pathway selected from the group consistingof benzoate degradation, glycerophospholipid metabolism, secondary bileacid biosynthesis, ppGpp biosynthesis, pyruvate fermentation to acetateand lactate, short chain fatty acid biosynthesis, biosynthesis ofansamycins, and starch degradation; andb) selecting said UC patient for a fecal microbe-based therapy, if therelative fecal abundance is above a pre-determined lowest limit.

Embodiment 54. A method for selecting a UC patient for a fecalmicrobe-based therapy, said method comprising

a) determining in a UC patient the relative fecal abundance of one ormore markers for a metabolic pathway selected from the group consistingof heme biosynthesis, lipopolysaccharide biosynthesis, ubiquinone andother terpenoid quinine biosynthesis, lysine biosynthesis, and oxidativephosphorylation pathway; andb) selecting said UC patient for a fecal microbe-based therapy, if therelative fecal abundance is below a pre-determined highest limit.

Embodiment 55. The method of any one of embodiments 51 to 54, furthercomprising subjecting said selected UC patient to a fecal microbe-basedtherapy.

EXAMPLES Example 1 Trial Design and Microbiome Characterization of aFMT-Based Therapy of UC

Patients with active UC are randomised in a double-blind controlledtrial to intensive multi-donor FMT or placebo enemas 5 days per week for8 weeks. Patients randomised to placebo are eligible to receiveopen-label FMT after the double-blind study period. FMT infusions areconstituted from the blended homogenised stool of 3 to 7 unrelateddonors, to increase microbial heterogeneity. Each patient receives alltheir FMT infusions from the same donor batch. See ClinicalTrials.gov atNCT01896635 and Paramsothy et al., Lancet 2017; 389: 1218-28, both ofwhich are incorporated by reference in their entirety.

Fecal samples are collected from individual donors, multi-donor FMTbatches and study patients for molecular microbiological analyses andgastrointestinal microbial community profiling. Donor fecal samples(n=105) are collected from the 14 individual donors (n=55) and the 21multi-donor FMT batches (n=50); eight samples are also taken from 4placebo batches to serve as control.

Seventy study patients provide a total of 314 fecal samples atscreening, then every 4 weeks during treatment (blinded, and open labelif applicable) and eight weeks after completing blinded or open-labelFMT therapy. These patients also contribute 160 colonoscopic large bowelbiopsies at study entry prior to treatment, after eight weeks of activeor placebo treatment (the primary study endpoint), and where relevantafter a further eight weeks of open-label treatment.

All samples are stored at -80° C. immediately after collection untilnucleic acid extraction. Fecal samples are homogenised and both DNA andRNA extracted using the MOBIO PowerViral RNA/DNA Isolation kit. FecalRNA is then isolated from DNA using the MOBIO On-Spin Column DNase kitand Bioline Isolate II RNA micro clean-up kit. Colonic biopsy samplesare homogenised and bacterial DNA and RNA extracted using theMacherey-Nagel RNA Isolation Kit. Colonic RNA is then isolated from DNAusing the MOBIO On-Spin Column DNase kit and Macherey-Nagel RNA clean-upkit. Fecal and colonic RNA is then converted to cDNA using the SensiFASTcDNA Synthesis Kit (Bioline).

The 16S rRNA gene fragment of the extracted DNA and RNA converted tocDNA is amplified using the Immolase DNA polymerase (95° C. for 10 min,35 cycles of 94° C. for 30 s 55° C. for 10 s, 72° C. for 45 s, followedby a final step of 72° C. for 10 min) and the primers F27-519R. Sampleindices and Illumina sequencing adapters are attached using the NexteraXT Index Kit according to the manufacturer's instructions. Ampliconsequencing is performed with the Illumina MiSeq Reagent kit v3 (2x300bp) at the Ramaciotti Centre for Genomics. Shotgun metagenomics isperformed on DNA extracted from 285 donor and patient fecal samplesusing Nextera XT DNA library prep kit and 2×250 bp HiSeq 2500 chemistry.This results in five datasets including fecal 16S DNA, fecal 16S cDNA,colonic biopsy 16S DNA, colonic biopsy 16S cDNA, and fecal shotgun DNA.

Quality filtering of 16S rRNA sequences is conducted using softwarepackage mothur (Schloss (2009). “Introducing mothur: open-source,platform-independent, community-supported software for describing andcomparing microbial communities.” Applied and Environmental Microbiology75(23): 7537-7541) and follows the mothur MiSeq SOP (Kozich (2013).“Development of a Dual-Index Sequencing Strategy and Curation Pipelinefor Analyzing Amplicon Sequence Data on the MiSeq Illumina SequencingPlatform.” Applied and Environmental Microbiology 79(17): 5112-5120).Paired-end sequences are merged into contigs, and poor quality contigsremoved based on alignment quality and ambiguous base calls. A multiplesequence alignment is constructed using the SILVA SEED 16S rRNAreference alignment (Quast The SILVA ribosomal RNA gene databaseproject: improved data processing and web-based tools. Nucleic Acids Res2013; 41: D590-6), and poorly aligned sequences removed. To eliminateartefacts of sequencing at high frequency, rare sequences with highsimilarity to abundant sequences are clustered together. Chimericsequences are removed using uchime (Edgar Bioinformatics, 2011; 27:2194-200). Sequences are taxonomically classified using the RibosomalDatabase project taxonomic outline (Wang Appl Environ Microbiol, 2007;73: 5261-7) and those without classification at the kingdom level(unknown) or classified as mitochondrial or chloroplast are removed.Quality filtered sequences are then clustered into operational taxonomicunits (OTUs) at 97% similarity using the opti-dust average neighbouralgorithm (Westcott OptiClust, an Improved Method for AssigningAmplicon-Based Sequence Data to Operational Taxonomic Units. mSphere2017;2 ), and consensus taxonomies of the OTUs obtained using theclassifications of sequences within each OTU. The resulting OTU count bysample data matrix is used for data analysis.

Shotgun metagenomic DNA sequence reads are first analysed with DeconSeq(Schmieder Fast identification and removal of sequence contaminationfrom genomic and metagenomic datasets. PLoS One 2011; 6:e17288) foridentification and filtering of human DNA sequences. Sequencing readsare assessed for quality using FastQC (version 0.11.2). SolexaQA is thenapplied to calculate sequence quality statistics and perform qualityfiltering of the Illumina reads. Paired-end raw reads are trimmed withthe BWA trimming mode at a threshold of Q13 (P=0.05) using the readtrimmer module DynamicTrim. Filtered reads that are less than 50 bp inlength are then discarded using LengthSort. The average microbial readcounts per sample are 4,590,171±119,145 reads. MetaPhlAn2 (Truong et al.MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods2015; 12: 902-3) is employed to generate taxonomic profiles from theshotgun reads, while HUMAnN2 (HMP Unified Metabolic Analysis Network)(Hall et al. A novel Ruminococcus gnavus clade enriched in inflammatorybowel disease patients. Genome medicine 2017; 9: 103) is used todetermine the metabolic contributions within the samples. The HUMAnN2pipeline involved mapping of the metagenomic reads against Unireforthologous gene family, MetCyc UniPathway, and KEGG.

During the initial double-blind FMT trial patients are allocated toactive FMT treatment or placebo groups (FMT: two levels—Placebo or FMT,factor type—fixed) and each patient is sampled at three time points overeight weeks (Time: three levels—0, 4 and 8 weeks, factor type—fixed).Each patient is included in the experimental design as a random factor.After 8 weeks, the initial placebo group receive active FMT and aresampled further at weeks 4 and 8 of the open-label (non-blind) period.All patients receiving active FMT are also sampled at 8 weeks aftercompleting active FMT therapy (blinded or open-label).

To examine which microbial taxa differed between patients showingremission, data are combined from the blinded and open-label studyperiods, and then groups are created based on remission (Remission, twolevels—Yes or No, factor type—fixed) and treatment group (FMT: threelevels—Placebo, FMTblind or FMTopen). We then examined the effect ofdifferent categories of remission, including remission within theblinded trial (Remission among Placebo and FMTblind), and regardless ofstudy phase (Remission among Placebo, FMTblind and FMTopen). Analysesare made using four different endpoint classifications—primary endpoint,clinical remission, endoscopic response, and endoscopic remission(steroid free endoscopic Mayo score of 0) (Paramsothy et al., Lancet2017; 389: 1218-28).

The effect of donor batch on remission is examined by allocating donorbatches into two groups based on the number of patient remissionsobserved for each batch (DonorRemission, two levels—Yes or No, factortype—fixed). If more than 50% of the patients receiving a particulardonor batch showed remission, the donor batch is allocated to theDonorRemission=Yes group, while all other donors are allocated to theDonorRemission=No group.

Microbial communities are examined with respect to the above analyses interms of alpha-diversity and beta-diversity, as well as comparing eachtaxon individually. Prior to diversity comparisons, the OTU counts arerarefied to account for uneven sequencing depths among samples(35,371,968 total clean reads; rarefied to 6447 clean reads/sample).Linear mixed models (LMMs) are used to examine the effects of thevarious predictors mentioned above. Models are created using the Rpackages LME4 (Bates et al., (2015). “Fitting Linear Mixed-EffectsModels Using lme4.” Journal of Statistical Software 2015 67(1): 48) andlmerTest (Kuznetsova et al., (2017). “lmerTest Package: Tests in LinearMixed Effects Models.” Journal of Statistical Software 82(13): 1 - 26).

The Bray-Curtis (BC) dissimilarity coefficient for beta-diversitycomparisons is employed, and prior to calculation of BC dissimilarities,OTU counts are transformed into square-root relative abundances. The BCdistance matrix is visualized using non-metric multidimensional scaling(nMDS). PERMANOVA is used to examine the effects of the variouspredictors mentioned above. Dissimilarities, Figures and models arecreated using the R package ‘vegan’ (Oksanen, (2017) Vegan: CommunityEcology Package). For per taxon comparisons, un-rarefied OTU counts areused in negative binomial generalised linear models (GLMs) with thesample totals used as an offset term. Contrasts are employed to examinethe comparisons of interest within each analysis. Models are createdusing the R package DESeq2 (Love et al., Moderated estimation of foldchange and dispersion for RNA-seq data with DESeq2.” Genome Biology15(12): 550). For confirmation, Linear Discriminant Analysis Effect Size(LEfSe) analyses are also performed (Segata et al. Metagenomic biomarkerdiscovery and explanation. Genome biology 2011; 12: R60).

Example 2 Specific Bacterial Taxa Associated with Therapeutic Outcome

Despite FMT therapy, five patients do not appear to have a major changein overall microbial structure, with their baseline samples clusteringtightly with their samples during and post-FMT. Surprisingly, one ofthese patients achieves the primary outcome, and on further analysis,their overall microbiota structure is similar at baseline and during andpost-FMT except for replacement of key species Bacteroides clarus (11.5%to 0.06%) and Akkermansia muciniphila (11.1% to 0%) withFaecalibacterium prausnitzii (4.9% to 11.1%), Eubacterium rectale (0.19%to 9.9%), and Eubacterium siraeum (0.96% to 14.2%).

To identify specific microbial taxa significantly associated withachieving or not achieving the primary outcome across all patients, theabundances of each OTU is modeled in each dataset using negativebinomial GLMs with remission as a predictor and presented the mostdiscriminating taxa as potential biomarkers. A range of microbial taxaassociated with lack of remission including Fusobacterium, Sutterella,Haemophilus, Escherichia, Megamonas, Clostridium cluster XIVa,Prevotella, Dialister, Veillonella and Bilophila, and these associationsare in some datasets clearer when blinded and open label patients arestratified. The most consistent association with lack of achievingprimary outcome is with Fusobacterium gonidiaformans, with this taxonidentified in fecal 16S rRNA gene, mucosal 16S rRNA gene and transcript,and shotgun sequencing data. Of interest, Prevotella OTU2 (Prevotellacopri in shotgun data) appears to flourish in several patients with FMT;however, this OTU is associated with lack of remission and patients whoachieve remission tend to be those who resist dominance by Prevotella,having lower levels relative to patients who do not achieve remission.

There is less consistency in taxa associated with remission across thedatasets—these most commonly involved members of Firmicutes e.g.Clostridium cluster XVIII, Ruminococcus, Lachnospiraceae, Roseburiainulinivorans, and Eubacterium hallii. The associations among a range ofthese microbial taxa and primary outcome are confirmed using LEfSe.

To further examine the consistency of these associations, GLMs is usedwith three other therapeutic outcomes including the stricter endpoint ofcomplete endoscopic remission (steroid free endoscopic Mayo 0),endoscopic response, and clinical remission. Fusobacteriumgonidiaformans, Sutterella wadsworthensis, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonellaand Bilophila are all consistently associated with lack of endoscopicremission. Analyses of endoscopic response and clinical remission areless consistent, likely due to the less strict nature of theseendpoints; however, a range of the above taxa (including Fusobacterium,Haemophilus, Escherichia, Dialister and Veillonella) are stillassociated with negative outcomes.

Example 3 FMT Results in Functional Changes Associated with TherapeuticOutcome

Microbial functional changes across FMT therapy and therapeutic outcomeare characterised, with analysis focusing on outputs from KEGG andMetaCyc pathways. FMT, but not placebo, resulted in significant changesin microbial KEGG (F_(1,42)=2.5, P=0.027) and MetaCyc pathways(F_(1,43)=2.3, P=0.010). Despite intense FMT, patient microbialfunctional profiles remain significantly different to that of the donors(475)=2.0, P=0.001, Permutations=999). Similar to the taxonomicprofiles, FMT increases homogeneity (reduced dispersion) in thefunctional profiles across patient samples, but not to the level ofindividual donors or donor batches. Due to the significant patientvariability that is observed in the data, a constraint on the factor‘patient’ is applied, which shows a clearer delineation between FMT andplacebo.

Specific pathways associated with primary outcome are then identifiedusing

GLMs. Pathways such as benzoate degradation, glycerophospholipidmetabolism, secondary bile acid biosynthesis, ppGpp biosynthesis,pyruvate fermentation to acetate and lactate (short chain fatty acidbiosynthesis), biosynthesis of ansamycins, and starch degradation areall associated with positive primary outcome. Taxa contributing tobeneficial pathways included Eubacterium, Ruminococcus, Lachnospiraceae,Roseburia, Dorea and Coprococcus, consistent with the taxonomic analysisassociating these species with positive therapeutic outcome.Furthermore, the relationship between short chain fatty acidbiosynthesis and positive primary outcome is confirmed in the predictedmetagenome (PICRUSt) of the mucosal microbiome. In contrast, hemebiosynthesis, lipopolysaccharide biosynthesis, ubiquinone and otherterpenoid quinine biosynthesis, lysine biosynthesis and oxidativephosphorylation pathways are all associated with negative primaryoutcome. The relationships between a range of these pathways and primaryoutcome are confirmed using LEfSe.

Similar to the taxonomic analysis, the analyses are replicated againstthe three other therapeutic outcomes of complete endoscopic remission,endoscopic response, and clinical remission. The results from theseendpoints show consistent associations as those observed for the primarystudy outcome.

Example 4 Donor Taxonomic and Functional Profiles Associated withTherapeutic Outcome

Despite FMT therapy over 8 weeks, patient taxonomic and functionalprofiles remain different to those of individual donors and donorbatches. Thus, specific factors associated with donor suitability areevaluated by analysis of the donor fecal samples (16S rRNA gene andtranscript, as well as shotgun metagenomic datasets) relative to thefour different therapeutic outcomes.

Donor batches are categorised based on the total number of samples andnumber of patients that achieved a positive primary outcome, with donorbatches leading to >50% remission classified as effective and the restas ineffective. α-diversity and β-diversity within effective andineffective batches are compared in all datasets, with no clear patternsemerging between the two groups. While some differences in globalβ-diversity are observed (F_(1,18)=1.7, P=0.071), this is likely due tothe high inter-donor variability.

Specific taxonomic differences between effective and ineffective batchesare then analysed using GLMs. Bacteroides OTU187 is in higher abundancein effective batches, and consistently Bacteroides fragilis, as well asBacteroides finegoldii, are identified as taxonomic markers in thesebatches. In contrast, Bacteroides uniformis and Bacteroides coprocolaare associated with ineffective batches. Other donor microbial taxaassociated with ineffective batches included Clostridium cluster XIVa(OTU173), a taxon that is associated with negative primary outcomes, andStreptococcus (OTU56), which is found in both the 16S rRNA gene andtranscript datasets.

No clear differences in global pathway compositions are found betweeneffective and ineffective batches. However, a range of pathways areidentified to be in higher abundance in either effective or ineffectivebatches. Specifically, pathways such as fatty acid biosynthesis andpropanoate metabolism are higher in effective batches while terpenoidbackbone biosynthesis and bacterial chemotaxis are higher in ineffectivebatches.

Similar analyses are conducted for the three other therapeuticendpoints. The strict endpoint of endoscopic remission and the lessstrict endpoint of endoscopic response showed similar outcomes to theprimary study endpoint. One notable difference is the clustering ofeffective batches at the higher end of α-diversity when shotguntaxonomic data is classified by endoscopic response. This higher levelof α-diversity is also identified for effective batches classified bythe clinical remission endpoint. In fact, classification of donor batcheffectiveness based on the clinical remission endpoint showed thestrongest signs of consistency with the results of the patient analysis.Sutterella wadsworthensis, previously associated with lack of remissionin patients, is associated with ineffective batches in clinicalremission. Further, pathways such as secondary bile acid biosynthesis,glycerophospholipid metabolism and biosynthesis of ansamycins are allassociated with positive patient outcomes and are associated witheffective batches. Moreover, heme biosynthesis is a strong marker fornegative primary outcome in patients and is higher in ineffectivebatches.

1. A pharmaceutical composition comprising viable non-pathogenicbacteria from one or more first microbial taxa selected from the groupconsisting of Clostridium cluster XVIII, Ruminococcus, Lachnospiraceae,Roseburia inulinivorans, Eubacterium hallii, and any combinationthereof, wherein said pharmaceutical composition contains no bacteriafrom one or more second microbial taxa selected from the groupconsisting of Fusobacterium, Sutterella, Haemophilus, Escherichia,Megamonas, Clostridium cluster XIVa, Prevotella, Dialister, Veillonella,and Bilophila.
 2. The pharmaceutical composition of claim 1, whereinsaid second microbial taxon is selected from the group consisting ofFusobacterium gonidiaformans, Prevotella copri, and Sutterellawadsworthensis.
 3. The pharmaceutical composition of claim 1, whereinsaid viable non-pathogenic bacteria is from a synthetic culture.
 4. Thepharmaceutical composition of claim 1, wherein said pharmaceuticalcomposition is in an anaerobic package or container.
 5. Thepharmaceutical composition of claim 1, wherein said pharmaceuticalcomposition is in a liquid, frozen, freeze-dried, spray-dried,lyophilized, or powder form.
 6. The pharmaceutical composition of claim1, wherein said pharmaceutical composition comprises an excipient, asaline, a buffer, a buffering agent, or a fluid-glucose-cellobiose agar(RGCA) media.
 7. The pharmaceutical composition of claim 1, wherein saidpharmaceutical composition comprises a cryoprotectant.
 8. Thepharmaceutical composition of claim 1, wherein said pharmaceuticalcomposition comprises a cryoprotectant comprising polyethylene glycol,skim milk, erythritol, arabitol, sorbitol, glucose, fructose, alanine,glycine, proline, sucrose, lactose, ribose, trehalose, dimethylsulfoxide (DMSO), glycerol, or a combination thereof.
 9. A method forproducing a pharmaceutical composition, said method comprising a)determining in a candidate fecal microbe source material the relativeabundance of one or more bacterial markers selected from the groupconsisting of Bacteroides OTU187, Bacteroides fragilis, Bacteroidesfinegoldii, Clostridium cluster XIVa (OTU173), Streptococcus (OTU56),Sutterella wadsworthensis, Bacteroides uniformis, and Bacteroidescoprocola; b) selecting said candidate fecal microbe source material ifthe relative abundance of Bacteroides OTU187, Bacteroides fragilis, orBacteroides finegoldii is above a pre-determined lowest limit, and/or ifthe relative abundance of Clostridium cluster XIVa (OTU173),Streptococcus (OTU56), Sutterella wadsworthensis, Bacteroides uniformis,or Bacteroides coprocola is below a pre-determined highest limit; and c)producing a pharmaceutical composition from said selected fecal microbesource material.
 10. The method of claim 9, wherein said pharmaceuticalcomposition is for treating UC.
 11. The method of claim 9, wherein saidfecal microbe source material is derived from one or more human donors.12. The method of claim 9, wherein said candidate fecal microbe sourcematerial is a substantially complete fecal microbiota from a donor. 13.A method for selecting a fecal microbe source material, said methodcomprising a) Determining in a candidate fecal microbe source materialthe relative abundance of one or more markers from a metabolic pathwayselected from the group consisting of fatty acid biosynthesis,propanoate metabolism, secondary bile acid biosynthesis,glycerophospholipid metabolism, biosynthesis of ansamycins, terpenoidbackbone biosynthesis, bacterial chemotaxis, heme biosynthesis, andshort chain fatty acid (SCFA) biosynthesis; and b) selecting saidcandidate fecal microbe source material based on the relative abundanceof said one or more markers.
 14. The method of claim 13, wherein saidfecal microbe source material is selected for producing a pharmaceuticalcomposition for treating UC.
 15. The method of claim 13, wherein saidone or more markers are metabolic markers.
 16. The method of claim 13,wherein said one or more markers comprise one or more metabolic pathwaygenes.
 17. The method of claim 13, wherein said relative abundance ofsaid one or more markers is above a pre-determined lowest limit, andsaid one or more markers are selected from the group consisting of fattyacid biosynthesis, propanoate metabolism, secondary bile acidbiosynthesis, glycerophospholipid metabolism, biosynthesis ofansamycins.
 18. The method of claim 13, wherein said relative abundanceof said one or more markers is below a pre-determined highest limit, andsaid one or more markers are selected from the group consisting ofterpenoid backbone biosynthesis, bacterial chemotaxis, and hemebiosynthesis.
 19. The method of claim 13, wherein said fecal microbesource material is derived from one or more human donors.
 20. The methodof claim 13, wherein said candidate fecal microbe source material is asubstantially complete fecal microbiota from a donor.